Karolina's Bioinformatics Portfolio
View the Project on GitHub akn006-navarro/bimm143_github_redo
Class 10 - Structural Bioinformatics
Karolina Navarro (PID: A19106745)
The PDB Statistics
The Protein Data Bank (PDB) is the main repository of biomolecular structures. Let’s see what it contains.
stats <- read.csv("Data Export Summary.csv")
stats
Molecular.Type X.ray EM NMR Integrative Multiple.methods
1 Protein (only) 178,795 21,825 12,773 343 226
2 Protein/Oligosaccharide 10,363 3,564 34 8 11
3 Protein/NA 9,106 6,335 287 24 7
4 Nucleic acid (only) 3,132 221 1,566 3 15
5 Other 175 25 33 4 0
6 Oligosaccharide (only) 11 0 6 0 1
Neutron Other Total
1 84 32 214,078
2 1 0 13,981
3 0 0 15,759
4 3 1 4,941
5 0 0 237
6 0 4 22
Q1: What percentage of structures in the PDB are solved by X-Ray and Electron Microscopy.
library(readr)
stats <- read_csv("Data Export Summary.csv")
Rows: 6 Columns: 9
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (1): Molecular Type
dbl (4): Integrative, Multiple methods, Neutron, Other
num (4): X-ray, EM, NMR, Total
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
stats
# A tibble: 6 × 9
`Molecular Type` `X-ray` EM NMR Integrative `Multiple methods` Neutron
<chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 Protein (only) 178795 21825 12773 343 226 84
2 Protein/Oligosacch… 10363 3564 34 8 11 1
3 Protein/NA 9106 6335 287 24 7 0
4 Nucleic acid (only) 3132 221 1566 3 15 3
5 Other 175 25 33 4 0 0
6 Oligosaccharide (o… 11 0 6 0 1 0
# ℹ 2 more variables: Other <dbl>, Total <dbl>
The comma in these numbers leads to the numbers here being read a character.
n.xray <- sum(stats$`X-ray`)
#n.em <-
n.total <- sum(stats$Total)
n.xray/n.total * 100
[1] 80.95077
Q2: What proportion of structures in the PDB are protein?
n.protein <- sum(stats$`Molecular Type` == "Protein (only)")
n.protein/n.total * 100
[1] 0.0004015774
Q3: SKIP
Q4: Water molecules normally have 3 atoms. Why do we see just one atom per water molecule in this structure?
Crystallographers model each water molecule as a single oxygen atom, labeled HOH, and omit the hydrogens.
Q5: There is a critical “conserved” water molecule in the binding site. Can you identify this water molecule? What residue number does this water molecule have
HOH 308
Visualizing the HIV-1 protease structure
We can use the Molstar viewer online: https://molstar.org/viewer/.
Q6: Generate and save a figure clearly showing the two distinct chains of HIV-protease along with the ligand. You might also consider showing the catalytic residues ASP 25 in each chain and the critical water (we recommend “Ball & Stick” for these side-chains). Add this figure to your Quarto document.
Q.7 OPTIONAL
A new clean image showing the catalytic ASP25 amino acids in both chains of the HIV-PR dimer along with the inhibitor an all important active site water.
Bio3D package for structural bioinformatics
##
library(bio3d)
pdb <- read.pdb("1hsg")
Note: Accessing on-line PDB file
pdb
Call: read.pdb(file = "1hsg")
Total Models#: 1
Total Atoms#: 1686, XYZs#: 5058 Chains#: 2 (values: A B)
Protein Atoms#: 1514 (residues/Calpha atoms#: 198)
Nucleic acid Atoms#: 0 (residues/phosphate atoms#: 0)
Non-protein/nucleic Atoms#: 172 (residues: 128)
Non-protein/nucleic resid values: [ HOH (127), MK1 (1) ]
Protein sequence:
PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYD
QILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNFPQITLWQRPLVTIKIGGQLKE
ALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTP
VNIIGRNLLTQIGCTLNF
+ attr: atom, xyz, seqres, helix, sheet,
calpha, remark, call
Q7: How many amino acid residues are there in this pdb object?
198
Q8: Name one of the two non-protein residues?
HOH (Water)
Q9: How many protein chains are in this structure?
Two
head(pdb$atom)
type eleno elety alt resid chain resno insert x y z o b
1 ATOM 1 N <NA> PRO A 1 <NA> 29.361 39.686 5.862 1 38.10
2 ATOM 2 CA <NA> PRO A 1 <NA> 30.307 38.663 5.319 1 40.62
3 ATOM 3 C <NA> PRO A 1 <NA> 29.760 38.071 4.022 1 42.64
4 ATOM 4 O <NA> PRO A 1 <NA> 28.600 38.302 3.676 1 43.40
5 ATOM 5 CB <NA> PRO A 1 <NA> 30.508 37.541 6.342 1 37.87
6 ATOM 6 CG <NA> PRO A 1 <NA> 29.296 37.591 7.162 1 38.40
segid elesy charge
1 <NA> N <NA>
2 <NA> C <NA>
3 <NA> C <NA>
4 <NA> O <NA>
5 <NA> C <NA>
6 <NA> C <NA>
#library(bio3dview)
#view.pdb(pdb)
#view.pdb(pdb, col="chain")
# Select the important ASP 25 residue
sele <- atom.select(pdb, resno=25)
# and highlight them in spacefill representation
#view.pdb(pdb, cols=c("navy","teal"),
# highlight = sele,
# highlight.style = "spacefill")
Predicting Functional Motions of a Single Structure
Read an ADK structure from the PDB database:
adk <- read.pdb("6s36")
Note: Accessing on-line PDB file
PDB has ALT records, taking A only, rm.alt=TRUE
adk
Call: read.pdb(file = "6s36")
Total Models#: 1
Total Atoms#: 1898, XYZs#: 5694 Chains#: 1 (values: A)
Protein Atoms#: 1654 (residues/Calpha atoms#: 214)
Nucleic acid Atoms#: 0 (residues/phosphate atoms#: 0)
Non-protein/nucleic Atoms#: 244 (residues: 244)
Non-protein/nucleic resid values: [ CL (3), HOH (238), MG (2), NA (1) ]
Protein sequence:
MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAAVKSGSELGKQAKDIMDAGKLVT
DELVIALVKERIAQEDCRNGFLLDGFPRTIPQADAMKEAGINVDYVLEFDVPDELIVDKI
VGRRVHAPSGRVYHVKFNPPKVEGKDDVTGEELTTRKDDQEETVRKRLVEYHQMTAPLIG
YYSKEAEAGNTKYAKVDGTKPVAEVRADLEKILG
+ attr: atom, xyz, seqres, helix, sheet,
calpha, remark, call
m <- nma(pdb)
Warning in nma.pdb(pdb): Possible multi-chain structure or missing in-structure residue(s) present
Fluctuations at neighboring positions may be affected.
Building Hessian... Done in 0.02 seconds.
Diagonalizing Hessian... Done in 0.26 seconds.
plot(m)
Write out our results as a wee trajectory/movie of predicted motion
#mktrj(m, file="adk_m7.pdb")
Comparitive Analysis with PCA
First Step is to find an ADK sequence:
library(bio3d)
id <- "1ake_A" ## Change this to run a different analysis
aa <- get.seq(id)
Warning in get.seq(id): Removing existing file: seqs.fasta
Fetching... Please wait. Done.
aa
1 . . . . . 60
pdb|1AKE|A MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAAVKSGSELGKQAKDIMDAGKLVT
1 . . . . . 60
61 . . . . . 120
pdb|1AKE|A DELVIALVKERIAQEDCRNGFLLDGFPRTIPQADAMKEAGINVDYVLEFDVPDELIVDRI
61 . . . . . 120
121 . . . . . 180
pdb|1AKE|A VGRRVHAPSGRVYHVKFNPPKVEGKDDVTGEELTTRKDDQEETVRKRLVEYHQMTAPLIG
121 . . . . . 180
181 . . . 214
pdb|1AKE|A YYSKEAEAGNTKYAKVDGTKPVAEVRADLEKILG
181 . . . 214
Call:
read.fasta(file = outfile)
Class:
fasta
Alignment dimensions:
1 sequence rows; 214 position columns (214 non-gap, 0 gap)
+ attr: id, ali, call
Next step, is search the PDB database for all related entries:
blast <- blast.pdb(aa)
Searching ... please wait (updates every 5 seconds) RID = V6B5HVE9016
..................................
Reporting 96 hits
hits <- plot(blast)
* Possible cutoff values: 260 3
Yielding Nhits: 20 96
* Chosen cutoff value of: 260
Yielding Nhits: 20
All of the BLAST results are in the PDB database for all related entries:
blast$hit.tbl
queryid subjectids identity alignmentlength mismatches gapopens
1 Query_5597383 1AKE_A 100.000 214 0 0
2 Query_5597383 8BQF_A 99.533 214 1 0
3 Query_5597383 4X8M_A 99.533 214 1 0
4 Query_5597383 6S36_A 99.533 214 1 0
5 Query_5597383 9R6U_A 99.533 214 1 0
6 Query_5597383 9R71_A 99.533 214 1 0
7 Query_5597383 8Q2B_A 99.533 214 1 0
8 Query_5597383 8RJ9_A 99.533 214 1 0
9 Query_5597383 6RZE_A 99.533 214 1 0
10 Query_5597383 4X8H_A 99.533 214 1 0
11 Query_5597383 3HPR_A 99.533 214 1 0
12 Query_5597383 1E4V_A 99.533 214 1 0
13 Query_5597383 5EJE_A 99.065 214 2 0
14 Query_5597383 1E4Y_A 99.065 214 2 0
15 Query_5597383 3X2S_A 98.598 214 3 0
16 Query_5597383 6HAP_A 98.131 214 4 0
17 Query_5597383 6HAM_A 97.196 214 6 0
18 Query_5597383 8PVW_A 84.579 214 6 2
19 Query_5597383 4K46_A 73.239 213 57 0
20 Query_5597383 4NP6_A 72.642 212 58 0
21 Query_5597383 3GMT_A 62.500 216 75 1
22 Query_5597383 4PZL_A 57.346 211 86 2
23 Query_5597383 5G3Y_A 55.505 218 88 2
24 Query_5597383 5G3Z_A 50.459 218 99 2
25 Query_5597383 5G40_A 49.541 218 101 2
26 Query_5597383 5X6J_A 50.000 218 98 3
27 Query_5597383 2C9Y_A 53.723 188 83 1
28 Query_5597383 1S3G_A 49.541 218 99 3
29 Query_5597383 9GR0_A 53.723 188 83 1
30 Query_5597383 9FL7_D 53.723 188 83 1
31 Query_5597383 1AK2_A 52.660 188 85 1
32 Query_5597383 3BE4_A 48.611 216 102 3
33 Query_5597383 1AKY_A 46.119 219 108 3
34 Query_5597383 3AKY_A 46.119 219 108 3
35 Query_5597383 3FB4_A 48.165 218 104 2
36 Query_5597383 4QBI_A 47.248 218 106 2
37 Query_5597383 1DVR_A 45.205 219 110 3
38 Query_5597383 3DKV_A 49.772 219 99 3
39 Query_5597383 3DL0_A 48.165 218 104 2
40 Query_5597383 1ZIN_A 45.413 218 110 2
41 Query_5597383 2P3S_A 47.248 218 106 2
42 Query_5597383 2EU8_A 47.248 218 106 2
43 Query_5597383 1P3J_A 47.248 218 106 2
44 Query_5597383 4QBF_A 49.772 219 99 3
45 Query_5597383 2ORI_A 47.248 218 106 2
46 Query_5597383 5X6I_A 46.789 218 107 2
47 Query_5597383 2QAJ_A 47.005 217 106 2
48 Query_5597383 2OO7_A 46.789 218 107 2
49 Query_5597383 2OSB_A 46.789 218 107 2
50 Query_5597383 4MKF_A 46.789 218 107 2
51 Query_5597383 3TLX_A 44.393 214 106 3
52 Query_5597383 4MKH_A 48.624 218 101 3
53 Query_5597383 4QBH_A 45.872 218 109 2
54 Query_5597383 4TYQ_A 48.165 218 102 3
55 Query_5597383 4QBG_B 47.248 218 104 3
56 Query_5597383 4TYP_A 47.248 218 104 3
57 Query_5597383 4JKY_A 44.037 218 103 5
58 Query_5597383 2RGX_A 43.578 218 104 4
59 Query_5597383 4JLO_A 43.578 218 104 5
60 Query_5597383 1ZAK_A 42.326 215 112 3
61 Query_5597383 1ZD8_A 43.915 189 96 3
62 Query_5597383 2AK3_A 44.324 185 101 2
63 Query_5597383 4NTZ_A 38.532 218 119 4
64 Query_5597383 2AR7_A 41.304 184 102 3
65 Query_5597383 3NDP_A 40.761 184 103 3
66 Query_5597383 1P4S_A 39.785 186 77 2
67 Query_5597383 2CDN_A 39.785 186 77 2
68 Query_5597383 3L0P_A 32.735 223 131 7
69 Query_5597383 5X6L_A 35.784 204 98 3
70 Query_5597383 2XB4_A 32.735 223 131 7
71 Query_5597383 5XRU_A 35.294 204 99 3
72 Query_5597383 5YCC_A 35.294 204 99 3
73 Query_5597383 5X6K_A 35.294 204 99 3
74 Query_5597383 5XZ2_A 33.962 212 107 3
75 Query_5597383 5YCF_A 34.906 212 105 3
76 Query_5597383 5YCB_A 34.804 204 100 3
77 Query_5597383 5YCD_A 36.464 181 87 2
78 Query_5597383 3ADK_A 36.066 183 89 3
79 Query_5597383 3UMF_A 33.333 186 92 3
80 Query_5597383 1Z83_A 34.973 183 91 3
81 Query_5597383 7X7S_A 34.973 183 91 3
82 Query_5597383 3CM0_A 34.434 212 106 5
83 Query_5597383 7DE3_A 36.066 183 89 5
84 Query_5597383 8X1G_A 34.426 183 92 3
85 Query_5597383 7N6G_6M 33.333 180 108 4
86 Query_5597383 1UKY_A 27.962 211 117 5
87 Query_5597383 1TEV_A 31.963 219 109 7
88 Query_5597383 7E9V_A 31.963 219 109 7
89 Query_5597383 2BWJ_A 30.851 188 98 4
90 Query_5597383 1QF9_A 27.907 215 117 5
91 Query_5597383 9FQR_Xf 30.645 124 83 2
93 Query_5597383 9FQR_Xc 28.800 125 56 4
94 Query_5597383 9D2F_D 29.032 124 56 4
95 Query_5597383 7N6G_6A 24.852 169 84 6
96 Query_5597383 9D2F_A 27.429 175 78 6
92 Query_5597383 9FQR_Xf 22.353 170 83 2
q.start q.end s.start s.end evalue bitscore positives mlog.evalue pdb.id
1 1 214 1 214 1.79e-156 432.0 100.00 358.621059 1AKE_A
2 1 214 21 234 2.93e-156 433.0 100.00 358.128272 8BQF_A
3 1 214 1 214 3.20e-156 432.0 100.00 358.040124 4X8M_A
4 1 214 1 214 4.71e-156 432.0 100.00 357.653587 6S36_A
5 1 214 1 214 1.05e-155 431.0 99.53 356.851899 9R6U_A
6 1 214 1 214 1.24e-155 431.0 99.53 356.685578 9R71_A
7 1 214 1 214 1.25e-155 431.0 99.53 356.677546 8Q2B_A
8 1 214 1 214 1.25e-155 431.0 99.53 356.677546 8RJ9_A
9 1 214 1 214 1.35e-155 431.0 99.53 356.600585 6RZE_A
10 1 214 1 214 1.78e-155 430.0 99.53 356.324076 4X8H_A
11 1 214 1 214 2.52e-155 430.0 99.53 355.976431 3HPR_A
12 1 214 1 214 2.66e-155 430.0 99.53 355.922363 1E4V_A
13 1 214 1 214 7.98e-155 429.0 99.07 354.823751 5EJE_A
14 1 214 1 214 4.62e-154 427.0 99.07 353.067710 1E4Y_A
15 1 214 1 214 7.73e-154 426.0 98.60 352.552995 3X2S_A
16 1 214 1 214 2.29e-153 425.0 98.60 351.466967 6HAP_A
17 1 214 1 214 4.68e-153 424.0 98.60 350.752221 6HAM_A
18 1 214 1 187 8.53e-122 344.0 85.05 278.771792 8PVW_A
19 1 213 1 213 2.08e-115 329.0 84.98 264.064918 4K46_A
20 2 213 5 216 1.15e-113 325.0 84.43 260.052354 4NP6_A
21 2 211 10 225 9.01e-90 265.0 71.30 205.034323 3GMT_A
22 2 209 26 235 2.15e-86 256.0 74.41 197.256850 4PZL_A
23 1 214 1 213 3.18e-76 230.0 68.81 173.839586 5G3Y_A
24 1 214 1 213 6.09e-73 221.0 69.27 166.282064 5G3Z_A
25 1 214 1 213 1.25e-70 216.0 68.35 160.957813 5G40_A
26 1 213 1 212 2.28e-68 210.0 65.60 155.751611 5X6J_A
27 1 184 17 204 1.15e-67 209.0 69.68 154.133439 2C9Y_A
28 1 213 1 212 1.18e-67 208.0 65.14 154.107687 1S3G_A
29 1 184 16 203 1.25e-67 209.0 69.68 154.050058 9GR0_A
30 1 184 22 209 1.68e-67 209.0 69.68 153.754407 9FL7_D
31 1 184 17 204 2.97e-67 207.0 70.21 153.184639 1AK2_A
32 2 213 7 217 7.97e-67 206.0 68.06 152.197517 3BE4_A
33 1 214 5 218 1.13e-66 206.0 65.75 151.848399 1AKY_A
34 1 214 5 218 1.37e-66 205.0 65.30 151.655805 3AKY_A
35 1 214 1 213 5.04e-66 204.0 65.14 150.353210 3FB4_A
36 1 214 1 213 2.44e-64 199.0 65.60 146.473448 4QBI_A
37 1 214 5 218 5.26e-64 199.0 64.84 145.705315 1DVR_A
38 1 214 1 213 2.83e-63 197.0 66.67 144.022584 3DKV_A
39 1 214 1 213 1.25e-62 195.0 66.97 142.537132 3DL0_A
40 1 214 1 213 1.39e-62 195.0 65.60 142.430972 1ZIN_A
41 1 214 1 213 2.10e-62 194.0 66.97 142.018338 2P3S_A
42 1 214 1 213 2.20e-62 194.0 66.97 141.971818 2EU8_A
43 1 214 1 213 2.98e-62 194.0 66.97 141.668352 1P3J_A
44 1 214 1 213 4.75e-62 194.0 66.21 141.202131 4QBF_A
45 1 214 1 213 7.44e-62 193.0 66.97 140.753405 2ORI_A
46 1 214 1 213 1.41e-61 192.0 66.51 140.114101 5X6I_A
47 1 213 1 212 1.52e-61 192.0 66.82 140.038980 2QAJ_A
48 1 214 1 213 1.78e-61 192.0 66.51 139.881077 2OO7_A
49 1 214 1 213 3.03e-61 192.0 66.51 139.349128 2OSB_A
50 1 214 1 213 3.38e-61 191.0 66.51 139.239815 4MKF_A
51 2 211 31 235 2.13e-60 190.0 64.95 137.398984 3TLX_A
52 1 213 3 214 2.18e-60 189.0 65.60 137.375781 4MKH_A
53 1 214 1 213 4.36e-60 189.0 64.68 136.682634 4QBH_A
54 1 213 1 212 5.36e-60 188.0 65.60 136.476142 4TYQ_A
55 1 213 1 212 9.38e-59 185.0 65.60 133.613941 4QBG_B
56 1 213 1 212 1.76e-58 184.0 65.14 132.984622 4TYP_A
57 1 214 1 203 8.10e-56 177.0 66.51 126.852901 4JKY_A
58 1 214 1 203 9.28e-56 177.0 65.60 126.716904 2RGX_A
59 1 214 1 203 2.77e-55 176.0 66.51 125.623333 4JLO_A
60 1 214 6 209 5.57e-54 173.0 63.72 122.622200 1ZAK_A
61 1 185 8 190 4.34e-50 164.0 64.55 113.661380 1ZD8_A
62 1 185 7 189 5.96e-50 163.0 65.41 113.344184 2AK3_A
63 1 213 6 213 2.13e-46 154.0 62.39 105.162792 4NTZ_A
64 1 182 28 207 7.50e-45 150.0 64.13 101.601426 2AR7_A
65 1 182 6 185 6.27e-44 148.0 63.59 99.477968 3NDP_A
66 1 182 1 155 1.04e-38 133.0 56.99 87.459013 1P4S_A
67 1 182 21 175 1.87e-38 133.0 56.99 86.872295 2CDN_A
68 1 209 1 218 4.01e-31 115.0 54.26 69.991347 3L0P_A
69 3 205 13 184 4.89e-31 114.0 52.45 69.792946 5X6L_A
70 1 209 1 218 5.29e-31 114.0 54.26 69.714320 2XB4_A
71 3 205 11 182 5.87e-31 113.0 52.45 69.610283 5XRU_A
72 3 205 11 182 6.90e-31 113.0 52.45 69.448616 5YCC_A
73 3 205 13 184 8.18e-31 113.0 52.45 69.278446 5X6K_A
74 3 213 13 192 9.65e-31 113.0 52.83 69.113180 5XZ2_A
75 3 213 11 190 9.83e-31 113.0 51.89 69.094699 5YCF_A
76 3 205 11 182 1.06e-30 113.0 52.45 69.019284 5YCB_A
77 3 182 11 164 2.81e-30 112.0 54.70 68.044368 5YCD_A
78 3 184 12 167 3.37e-30 111.0 54.10 67.862640 3ADK_A
79 3 185 32 188 1.78e-29 110.0 56.45 66.198354 3UMF_A
80 3 184 12 167 2.09e-29 109.0 54.64 66.037804 1Z83_A
81 3 184 16 171 2.48e-29 109.0 54.64 65.866709 7X7S_A
82 3 214 7 185 1.01e-28 107.0 50.94 64.462432 3CM0_A
83 3 184 11 166 1.33e-28 107.0 56.28 64.187204 7DE3_A
84 3 184 11 166 1.67e-28 107.0 54.10 63.959559 8X1G_A
85 1 168 1239 1418 1.73e-25 105.0 53.33 57.016506 7N6G_6
86 3 210 18 196 1.09e-24 97.8 53.55 55.175865 1UKY_A
87 3 213 6 192 7.71e-24 95.5 49.77 53.219524 1TEV_A
88 3 213 24 210 1.20e-23 95.5 49.77 52.777136 7E9V_A
89 3 187 15 173 7.97e-22 90.1 49.47 48.581188 2BWJ_A
90 3 213 9 189 3.10e-20 85.9 47.44 44.920300 1QF9_A
91 1 121 1411 1534 2.10e-08 55.5 50.00 17.678743 9FQR_x
93 1 93 368 491 6.74e-07 50.8 46.40 14.210036 9FQR_x
94 1 93 368 490 3.39e-06 48.9 45.16 12.594681 9D2F_D
95 76 207 760 922 1.44e-05 47.0 42.01 11.148282 7N6G_6
96 1 126 976 1150 6.00e-03 39.3 42.29 5.115996 9D2F_A
92 1 121 991 1160 2.30e-02 37.4 37.65 3.772261 9FQR_x
acc
1 1AKE_A
2 8BQF_A
3 4X8M_A
4 6S36_A
5 9R6U_A
6 9R71_A
7 8Q2B_A
8 8RJ9_A
9 6RZE_A
10 4X8H_A
11 3HPR_A
12 1E4V_A
13 5EJE_A
14 1E4Y_A
15 3X2S_A
16 6HAP_A
17 6HAM_A
18 8PVW_A
19 4K46_A
20 4NP6_A
21 3GMT_A
22 4PZL_A
23 5G3Y_A
24 5G3Z_A
25 5G40_A
26 5X6J_A
27 2C9Y_A
28 1S3G_A
29 9GR0_A
30 9FL7_D
31 1AK2_A
32 3BE4_A
33 1AKY_A
34 3AKY_A
35 3FB4_A
36 4QBI_A
37 1DVR_A
38 3DKV_A
39 3DL0_A
40 1ZIN_A
41 2P3S_A
42 2EU8_A
43 1P3J_A
44 4QBF_A
45 2ORI_A
46 5X6I_A
47 2QAJ_A
48 2OO7_A
49 2OSB_A
50 4MKF_A
51 3TLX_A
52 4MKH_A
53 4QBH_A
54 4TYQ_A
55 4QBG_B
56 4TYP_A
57 4JKY_A
58 2RGX_A
59 4JLO_A
60 1ZAK_A
61 1ZD8_A
62 2AK3_A
63 4NTZ_A
64 2AR7_A
65 3NDP_A
66 1P4S_A
67 2CDN_A
68 3L0P_A
69 5X6L_A
70 2XB4_A
71 5XRU_A
72 5YCC_A
73 5X6K_A
74 5XZ2_A
75 5YCF_A
76 5YCB_A
77 5YCD_A
78 3ADK_A
79 3UMF_A
80 1Z83_A
81 7X7S_A
82 3CM0_A
83 7DE3_A
84 8X1G_A
85 7N6G_6M
86 1UKY_A
87 1TEV_A
88 7E9V_A
89 2BWJ_A
90 1QF9_A
91 9FQR_Xf
93 9FQR_Xc
94 9D2F_D
95 7N6G_6A
96 9D2F_A
92 9FQR_Xf
The “top hits” are in the hits object. Now we can download these to
our computer. Put these in the a wee sub-folder (directory) called
“pdbs” and use gzip to speed things up.
#Download related PDB files
files <- get.pdb(hits$pdb.id, path="pdbs", split=TRUE, gzip=TRUE)
Warning in get.pdb(hits$pdb.id, path = "pdbs", split = TRUE, gzip = TRUE):
pdbs/1AKE.pdb exists. Skipping download
Warning in get.pdb(hits$pdb.id, path = "pdbs", split = TRUE, gzip = TRUE):
pdbs/8BQF.pdb exists. Skipping download
Warning in get.pdb(hits$pdb.id, path = "pdbs", split = TRUE, gzip = TRUE):
pdbs/4X8M.pdb exists. Skipping download
Warning in get.pdb(hits$pdb.id, path = "pdbs", split = TRUE, gzip = TRUE):
pdbs/6S36.pdb exists. Skipping download
Warning in get.pdb(hits$pdb.id, path = "pdbs", split = TRUE, gzip = TRUE):
pdbs/9R6U.pdb exists. Skipping download
Warning in get.pdb(hits$pdb.id, path = "pdbs", split = TRUE, gzip = TRUE):
pdbs/9R71.pdb exists. Skipping download
Warning in get.pdb(hits$pdb.id, path = "pdbs", split = TRUE, gzip = TRUE):
pdbs/8Q2B.pdb exists. Skipping download
Warning in get.pdb(hits$pdb.id, path = "pdbs", split = TRUE, gzip = TRUE):
pdbs/8RJ9.pdb exists. Skipping download
Warning in get.pdb(hits$pdb.id, path = "pdbs", split = TRUE, gzip = TRUE):
pdbs/6RZE.pdb exists. Skipping download
Warning in get.pdb(hits$pdb.id, path = "pdbs", split = TRUE, gzip = TRUE):
pdbs/4X8H.pdb exists. Skipping download
Warning in get.pdb(hits$pdb.id, path = "pdbs", split = TRUE, gzip = TRUE):
pdbs/3HPR.pdb exists. Skipping download
Warning in get.pdb(hits$pdb.id, path = "pdbs", split = TRUE, gzip = TRUE):
pdbs/1E4V.pdb exists. Skipping download
Warning in get.pdb(hits$pdb.id, path = "pdbs", split = TRUE, gzip = TRUE):
pdbs/5EJE.pdb exists. Skipping download
Warning in get.pdb(hits$pdb.id, path = "pdbs", split = TRUE, gzip = TRUE):
pdbs/1E4Y.pdb exists. Skipping download
Warning in get.pdb(hits$pdb.id, path = "pdbs", split = TRUE, gzip = TRUE):
pdbs/3X2S.pdb exists. Skipping download
Warning in get.pdb(hits$pdb.id, path = "pdbs", split = TRUE, gzip = TRUE):
pdbs/6HAP.pdb exists. Skipping download
Warning in get.pdb(hits$pdb.id, path = "pdbs", split = TRUE, gzip = TRUE):
pdbs/6HAM.pdb exists. Skipping download
Warning in get.pdb(hits$pdb.id, path = "pdbs", split = TRUE, gzip = TRUE):
pdbs/8PVW.pdb exists. Skipping download
Warning in get.pdb(hits$pdb.id, path = "pdbs", split = TRUE, gzip = TRUE):
pdbs/4K46.pdb exists. Skipping download
Warning in get.pdb(hits$pdb.id, path = "pdbs", split = TRUE, gzip = TRUE):
pdbs/4NP6.pdb exists. Skipping download
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These look like a hot mess!
Next we will use the pdbaln() function to align and also optionally
fit (i.e. superpose) the identified PDB structures.
This requires a BioConductor package called “msa” that we need to
install. First we install BiocManager. Then we use
BiocManager::install("msa")
# Align related PDBs
pdbs <- pdbaln(files, fit = TRUE, exefile="msa")
Reading PDB files:
pdbs/split_chain/1AKE_A.pdb
pdbs/split_chain/8BQF_A.pdb
pdbs/split_chain/4X8M_A.pdb
pdbs/split_chain/6S36_A.pdb
pdbs/split_chain/9R6U_A.pdb
pdbs/split_chain/9R71_A.pdb
pdbs/split_chain/8Q2B_A.pdb
pdbs/split_chain/8RJ9_A.pdb
pdbs/split_chain/6RZE_A.pdb
pdbs/split_chain/4X8H_A.pdb
pdbs/split_chain/3HPR_A.pdb
pdbs/split_chain/1E4V_A.pdb
pdbs/split_chain/5EJE_A.pdb
pdbs/split_chain/1E4Y_A.pdb
pdbs/split_chain/3X2S_A.pdb
pdbs/split_chain/6HAP_A.pdb
pdbs/split_chain/6HAM_A.pdb
pdbs/split_chain/8PVW_A.pdb
pdbs/split_chain/4K46_A.pdb
pdbs/split_chain/4NP6_A.pdb
PDB has ALT records, taking A only, rm.alt=TRUE
. PDB has ALT records, taking A only, rm.alt=TRUE
.. PDB has ALT records, taking A only, rm.alt=TRUE
. PDB has ALT records, taking A only, rm.alt=TRUE
. PDB has ALT records, taking A only, rm.alt=TRUE
. PDB has ALT records, taking A only, rm.alt=TRUE
. PDB has ALT records, taking A only, rm.alt=TRUE
. PDB has ALT records, taking A only, rm.alt=TRUE
.. PDB has ALT records, taking A only, rm.alt=TRUE
.. PDB has ALT records, taking A only, rm.alt=TRUE
.... PDB has ALT records, taking A only, rm.alt=TRUE
. PDB has ALT records, taking A only, rm.alt=TRUE
. PDB has ALT records, taking A only, rm.alt=TRUE
..
Extracting sequences
pdb/seq: 1 name: pdbs/split_chain/1AKE_A.pdb
PDB has ALT records, taking A only, rm.alt=TRUE
pdb/seq: 2 name: pdbs/split_chain/8BQF_A.pdb
PDB has ALT records, taking A only, rm.alt=TRUE
pdb/seq: 3 name: pdbs/split_chain/4X8M_A.pdb
pdb/seq: 4 name: pdbs/split_chain/6S36_A.pdb
PDB has ALT records, taking A only, rm.alt=TRUE
pdb/seq: 5 name: pdbs/split_chain/9R6U_A.pdb
PDB has ALT records, taking A only, rm.alt=TRUE
pdb/seq: 6 name: pdbs/split_chain/9R71_A.pdb
PDB has ALT records, taking A only, rm.alt=TRUE
pdb/seq: 7 name: pdbs/split_chain/8Q2B_A.pdb
PDB has ALT records, taking A only, rm.alt=TRUE
pdb/seq: 8 name: pdbs/split_chain/8RJ9_A.pdb
PDB has ALT records, taking A only, rm.alt=TRUE
pdb/seq: 9 name: pdbs/split_chain/6RZE_A.pdb
PDB has ALT records, taking A only, rm.alt=TRUE
pdb/seq: 10 name: pdbs/split_chain/4X8H_A.pdb
pdb/seq: 11 name: pdbs/split_chain/3HPR_A.pdb
PDB has ALT records, taking A only, rm.alt=TRUE
pdb/seq: 12 name: pdbs/split_chain/1E4V_A.pdb
pdb/seq: 13 name: pdbs/split_chain/5EJE_A.pdb
PDB has ALT records, taking A only, rm.alt=TRUE
pdb/seq: 14 name: pdbs/split_chain/1E4Y_A.pdb
pdb/seq: 15 name: pdbs/split_chain/3X2S_A.pdb
pdb/seq: 16 name: pdbs/split_chain/6HAP_A.pdb
pdb/seq: 17 name: pdbs/split_chain/6HAM_A.pdb
PDB has ALT records, taking A only, rm.alt=TRUE
pdb/seq: 18 name: pdbs/split_chain/8PVW_A.pdb
PDB has ALT records, taking A only, rm.alt=TRUE
pdb/seq: 19 name: pdbs/split_chain/4K46_A.pdb
PDB has ALT records, taking A only, rm.alt=TRUE
pdb/seq: 20 name: pdbs/split_chain/4NP6_A.pdb
Have a wee peek at this new “align object” pdbs
pdbs
1 . . . 40
[Truncated_Name:1]1AKE_A.pdb --MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAA
[Truncated_Name:2]8BQF_A.pdb --MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAA
[Truncated_Name:3]4X8M_A.pdb --MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAA
[Truncated_Name:4]6S36_A.pdb --MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAA
[Truncated_Name:5]9R6U_A.pdb --MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAA
[Truncated_Name:6]9R71_A.pdb --MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAA
[Truncated_Name:7]8Q2B_A.pdb --MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAA
[Truncated_Name:8]8RJ9_A.pdb --MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAA
[Truncated_Name:9]6RZE_A.pdb --MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAA
[Truncated_Name:10]4X8H_A.pdb --MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAA
[Truncated_Name:11]3HPR_A.pdb --MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAA
[Truncated_Name:12]1E4V_A.pdb --MRIILLGAPVAGKGTQAQFIMEKYGIPQISTGDMLRAA
[Truncated_Name:13]5EJE_A.pdb --MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAA
[Truncated_Name:14]1E4Y_A.pdb --MRIILLGALVAGKGTQAQFIMEKYGIPQISTGDMLRAA
[Truncated_Name:15]3X2S_A.pdb --MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAA
[Truncated_Name:16]6HAP_A.pdb --MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAA
[Truncated_Name:17]6HAM_A.pdb --MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAA
[Truncated_Name:18]8PVW_A.pdb --MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAA
[Truncated_Name:19]4K46_A.pdb --MRIILLGAPGAGKGTQAQFIMAKFGIPQISTGDMLRAA
[Truncated_Name:20]4NP6_A.pdb NAMRIILLGAPGAGKGTQAQFIMEKFGIPQISTGDMLRAA
******** *********** *^**************
1 . . . 40
41 . . . 80
[Truncated_Name:1]1AKE_A.pdb VKSGSELGKQAKDIMDAGKLVTDELVIALVKERIAQEDCR
[Truncated_Name:2]8BQF_A.pdb VKSGSELGKQAKDIMDAGKLVTDELVIALVKERIAQE---
[Truncated_Name:3]4X8M_A.pdb VKSGSELGKQAKDIMDAGKLVTDELVIALVKERIAQEDCR
[Truncated_Name:4]6S36_A.pdb VKSGSELGKQAKDIMDAGKLVTDELVIALVKERIAQEDCR
[Truncated_Name:5]9R6U_A.pdb VKSGSELGAQAKDIMDAGKLVTDELVIALVKERIAQEDCR
[Truncated_Name:6]9R71_A.pdb VKSGSELGKQAKDIMDAGKLVTDELVIALVKERIAQEDCR
[Truncated_Name:7]8Q2B_A.pdb VKSGSELGKQAKDIMDAGKLVTDELVIALVKERIAQEDCR
[Truncated_Name:8]8RJ9_A.pdb VKSGSELGKQAKDIMDAGKLVTDELVIALVKERIAQEDCR
[Truncated_Name:9]6RZE_A.pdb VKSGSELGKQAKDIMDAGKLVTDELVIALVKERIAQEDCR
[Truncated_Name:10]4X8H_A.pdb VKSGSELGKQAKDIMDAGKLVTDELVIALVKERIAQEDCR
[Truncated_Name:11]3HPR_A.pdb VKSGSELGKQAKDIMDAGKLVTDELVIALVKERIAQEDCR
[Truncated_Name:12]1E4V_A.pdb VKSGSELGKQAKDIMDAGKLVTDELVIALVKERIAQEDCR
[Truncated_Name:13]5EJE_A.pdb VKSGSELGKQAKDIMDACKLVTDELVIALVKERIAQEDCR
[Truncated_Name:14]1E4Y_A.pdb VKSGSELGKQAKDIMDAGKLVTDELVIALVKERIAQEDCR
[Truncated_Name:15]3X2S_A.pdb VKSGSELGKQAKDIMDCGKLVTDELVIALVKERIAQEDSR
[Truncated_Name:16]6HAP_A.pdb VKSGSELGKQAKDIMDAGKLVTDELVIALVRERICQEDSR
[Truncated_Name:17]6HAM_A.pdb IKSGSELGKQAKDIMDAGKLVTDEIIIALVKERICQEDSR
[Truncated_Name:18]8PVW_A.pdb VKSGSELGKQAKDIMDAGKLVTDELVIALVKERIAQEDCR
[Truncated_Name:19]4K46_A.pdb IKAGTELGKQAKSVIDAGQLVSDDIILGLVKERIAQDDCA
[Truncated_Name:20]4NP6_A.pdb IKAGTELGKQAKAVIDAGQLVSDDIILGLIKERIAQADCE
^* *^*** *** ^^* **^*^^^^^*^^*** *
41 . . . 80
81 . . . 120
[Truncated_Name:1]1AKE_A.pdb NGFLLDGFPRTIPQADAMKEAGINVDYVLEFDVPDELIVD
[Truncated_Name:2]8BQF_A.pdb -GFLLDGFPRTIPQADAMKEAGINVDYVIEFDVPDELIVD
[Truncated_Name:3]4X8M_A.pdb NGFLLDGFPRTIPQADAMKEAGINVDYVLEFDVPDELIVD
[Truncated_Name:4]6S36_A.pdb NGFLLDGFPRTIPQADAMKEAGINVDYVLEFDVPDELIVD
[Truncated_Name:5]9R6U_A.pdb NGFLLDGFPRTIPQADAMKEAGINVDYVLEFDVPDELIVD
[Truncated_Name:6]9R71_A.pdb NGFLLDGFPRTIPQADAMKEAGINVDYVLEFDVPDALIVD
[Truncated_Name:7]8Q2B_A.pdb NGFLLDGFPRTIPQADAMKEAGINVDYVLEFDVPDELIVD
[Truncated_Name:8]8RJ9_A.pdb NGFLLAGFPRTIPQADAMKEAGINVDYVLEFDVPDELIVD
[Truncated_Name:9]6RZE_A.pdb NGFLLDGFPRTIPQADAMKEAGINVDYVLEFDVPDELIVD
[Truncated_Name:10]4X8H_A.pdb NGFLLDGFPRTIPQADAMKEAGINVDYVLEFDVPDELIVD
[Truncated_Name:11]3HPR_A.pdb NGFLLDGFPRTIPQADAMKEAGINVDYVLEFDVPDELIVD
[Truncated_Name:12]1E4V_A.pdb NGFLLDGFPRTIPQADAMKEAGINVDYVLEFDVPDELIVD
[Truncated_Name:13]5EJE_A.pdb NGFLLDGFPRTIPQADAMKEAGINVDYVLEFDVPDELIVD
[Truncated_Name:14]1E4Y_A.pdb NGFLLDGFPRTIPQADAMKEAGINVDYVLEFDVPDELIVD
[Truncated_Name:15]3X2S_A.pdb NGFLLDGFPRTIPQADAMKEAGINVDYVLEFDVPDELIVD
[Truncated_Name:16]6HAP_A.pdb NGFLLDGFPRTIPQADAMKEAGINVDYVLEFDVPDELIVD
[Truncated_Name:17]6HAM_A.pdb NGFLLDGFPRTIPQADAMKEAGINVDYVLEFDVPDELIVD
[Truncated_Name:18]8PVW_A.pdb NGFLLDGFPRTIPQADAMKEAGINVDYVLEFDVPDELIVD
[Truncated_Name:19]4K46_A.pdb KGFLLDGFPRTIPQADGLKEVGVVVDYVIEFDVADSVIVE
[Truncated_Name:20]4NP6_A.pdb KGFLLDGFPRTIPQADGLKEMGINVDYVIEFDVADDVIVE
**** **********^^** *^ ****^**** * ^**^
81 . . . 120
121 . . . 160
[Truncated_Name:1]1AKE_A.pdb RIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTGEELTTRKD
[Truncated_Name:2]8BQF_A.pdb RIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTGEELTTRKD
[Truncated_Name:3]4X8M_A.pdb RIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTGEELTTRKD
[Truncated_Name:4]6S36_A.pdb KIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTGEELTTRKD
[Truncated_Name:5]9R6U_A.pdb RIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTGEELTTRKD
[Truncated_Name:6]9R71_A.pdb RIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTGEELTTRKD
[Truncated_Name:7]8Q2B_A.pdb RIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTGEELTTRKA
[Truncated_Name:8]8RJ9_A.pdb RIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTGEELTTRKD
[Truncated_Name:9]6RZE_A.pdb AIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTGEELTTRKD
[Truncated_Name:10]4X8H_A.pdb RIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTGEELTTRKD
[Truncated_Name:11]3HPR_A.pdb RIVGRRVHAPSGRVYHVKFNPPKVEGKDDGTGEELTTRKD
[Truncated_Name:12]1E4V_A.pdb RIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTGEELTTRKD
[Truncated_Name:13]5EJE_A.pdb RIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTGEELTTRKD
[Truncated_Name:14]1E4Y_A.pdb RIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTGEELTTRKD
[Truncated_Name:15]3X2S_A.pdb RIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTGEELTTRKD
[Truncated_Name:16]6HAP_A.pdb RIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTGEELTTRKD
[Truncated_Name:17]6HAM_A.pdb RIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTGEELTTRKD
[Truncated_Name:18]8PVW_A.pdb RILKR--GETSGRV-------------------------D
[Truncated_Name:19]4K46_A.pdb RMAGRRAHLASGRTYHNVYNPPKVEGKDDVTGEDLVIRED
[Truncated_Name:20]4NP6_A.pdb RMAGRRAHLPSGRTYHVVYNPPKVEGKDDVTGEDLVIRED
^ * ***
121 . . . 160
161 . . . 200
[Truncated_Name:1]1AKE_A.pdb DQEETVRKRLVEYHQMTAPLIGYYSKEAEAGNTKYAKVDG
[Truncated_Name:2]8BQF_A.pdb DQEETVRKRLVEYHQMTAPLIGYYSKEAEAGNTKYAKVDG
[Truncated_Name:3]4X8M_A.pdb DQEETVRKRLVEWHQMTAPLIGYYSKEAEAGNTKYAKVDG
[Truncated_Name:4]6S36_A.pdb DQEETVRKRLVEYHQMTAPLIGYYSKEAEAGNTKYAKVDG
[Truncated_Name:5]9R6U_A.pdb DQEETVRKRLVEYHQMTAPLIGYYSKEAEAGNTKYAKVDG
[Truncated_Name:6]9R71_A.pdb DQEETVRKRLVEYHQMTAPLIGYYSKEAEAGNTKYAKVDG
[Truncated_Name:7]8Q2B_A.pdb DQEETVRKRLVEYHQMTAPLIGYYSKEAEAGNTKYAKVDG
[Truncated_Name:8]8RJ9_A.pdb DQEETVRKRLVEYHQMTAPLIGYYSKEAEAGNTKYAKVDG
[Truncated_Name:9]6RZE_A.pdb DQEETVRKRLVEYHQMTAPLIGYYSKEAEAGNTKYAKVDG
[Truncated_Name:10]4X8H_A.pdb DQEETVRKRLVEYHQMTAALIGYYSKEAEAGNTKYAKVDG
[Truncated_Name:11]3HPR_A.pdb DQEETVRKRLVEYHQMTAPLIGYYSKEAEAGNTKYAKVDG
[Truncated_Name:12]1E4V_A.pdb DQEETVRKRLVEYHQMTAPLIGYYSKEAEAGNTKYAKVDG
[Truncated_Name:13]5EJE_A.pdb DQEECVRKRLVEYHQMTAPLIGYYSKEAEAGNTKYAKVDG
[Truncated_Name:14]1E4Y_A.pdb DQEETVRKRLVEYHQMTAPLIGYYSKEAEAGNTKYAKVDG
[Truncated_Name:15]3X2S_A.pdb DQEETVRKRLCEYHQMTAPLIGYYSKEAEAGNTKYAKVDG
[Truncated_Name:16]6HAP_A.pdb DQEETVRKRLVEYHQMTAPLIGYYSKEAEAGNTKYAKVDG
[Truncated_Name:17]6HAM_A.pdb DQEETVRKRLVEYHQMTAPLIGYYSKEAEAGNTKYAKVDG
[Truncated_Name:18]8PVW_A.pdb DNEETVRKRLVEYHQMTAPLIGYYSKEAEAGNTKYAKVDG
[Truncated_Name:19]4K46_A.pdb DKEETVLARLGVYHNQTAPLIAYYGKEAEAGNTQYLKFDG
[Truncated_Name:20]4NP6_A.pdb DKEETVRARLNVYHTQTAPLIEYYGKEAAAGKTQYLKFDG
* ** * ** ^* ** ** ** *** ** * * * **
161 . . . 200
201 . 216
[Truncated_Name:1]1AKE_A.pdb TKPVAEVRADLEKILG
[Truncated_Name:2]8BQF_A.pdb TKPVAEVRADLEKIL-
[Truncated_Name:3]4X8M_A.pdb TKPVAEVRADLEKILG
[Truncated_Name:4]6S36_A.pdb TKPVAEVRADLEKILG
[Truncated_Name:5]9R6U_A.pdb TKPVAEVRADLEKILG
[Truncated_Name:6]9R71_A.pdb TKPVAEVRADLEKILG
[Truncated_Name:7]8Q2B_A.pdb TKPVAEVRADLEKILG
[Truncated_Name:8]8RJ9_A.pdb TKPVAEVRADLEKILG
[Truncated_Name:9]6RZE_A.pdb TKPVAEVRADLEKILG
[Truncated_Name:10]4X8H_A.pdb TKPVAEVRADLEKILG
[Truncated_Name:11]3HPR_A.pdb TKPVAEVRADLEKILG
[Truncated_Name:12]1E4V_A.pdb TKPVAEVRADLEKILG
[Truncated_Name:13]5EJE_A.pdb TKPVAEVRADLEKILG
[Truncated_Name:14]1E4Y_A.pdb TKPVAEVRADLEKILG
[Truncated_Name:15]3X2S_A.pdb TKPVAEVRADLEKILG
[Truncated_Name:16]6HAP_A.pdb TKPVCEVRADLEKILG
[Truncated_Name:17]6HAM_A.pdb TKPVCEVRADLEKILG
[Truncated_Name:18]8PVW_A.pdb TKPVAEVRADLEKILG
[Truncated_Name:19]4K46_A.pdb TKAVAEVSAELEKALA
[Truncated_Name:20]4NP6_A.pdb TKQVSEVSADIAKALA
** * ** *^^ * *
201 . 216
Call:
pdbaln(files = files, fit = TRUE, exefile = "msa")
Class:
pdbs, fasta
Alignment dimensions:
20 sequence rows; 216 position columns (182 non-gap, 34 gap)
+ attr: xyz, resno, b, chain, id, ali, resid, sse, call
We could view these in R with bio3dview view.pdbs() function.
Code if having loaded this package previously: * library(bio3dview) view.pdbs(pdbs)
PCA
We can run PCA on our pdbs object using the pca() function from
bio3d:
pc.xray <- pca(pdbs)
plot(pc.xray)
plot(pc.xray, 1:2)
We can make a visualization of the major conformational difference
(i.e. large scale structure change) captured by our PCA analysis with
the mktrj() function.
pc1 <- mktrj(pc.xray, file = "pca.pdb")
Let’s see in Mol-Star