Bioinformatics
Fall23 Barry Grant Bioinformatics
class11
DAR pID: A69026881
At the time of writing there are 183201 protein structures. In UniProt there are 251600768 protein seqs/
pdb <- read.csv("~/Desktop/Data Export Summary.csv", row.names = 1)
head(pdb)
X.ray EM NMR Multiple.methods Neutron Other
Protein (only) 158,844 11,759 12,296 197 73 32
Protein/Oligosaccharide 9,260 2,054 34 8 1 0
Protein/NA 8,307 3,667 284 7 0 0
Nucleic acid (only) 2,730 113 1,467 13 3 1
Other 164 9 32 0 0 0
Oligosaccharide (only) 11 0 6 1 0 4
Total
Protein (only) 183,201
Protein/Oligosaccharide 11,357
Protein/NA 12,265
Nucleic acid (only) 4,327
Other 205
Oligosaccharide (only) 22
round(183201/251600768*100, 2)
[1] 0.07
#make character values in pdb df into numeric values
#i.e. take out the commas
remove_commas <- function(df) {
df[] <- lapply(df, function(x) gsub(",", "", x))
return(df)
}
pdb <- remove_commas(pdb)
pdb <- sapply(pdb, as.numeric)
head(pdb)
X.ray EM NMR Multiple.methods Neutron Other Total
[1,] 158844 11759 12296 197 73 32 183201
[2,] 9260 2054 34 8 1 0 11357
[3,] 8307 3667 284 7 0 0 12265
[4,] 2730 113 1467 13 3 1 4327
[5,] 164 9 32 0 0 0 205
[6,] 11 0 6 1 0 4 22
totals <- apply(pdb, 2, sum)
totals
X.ray EM NMR Multiple.methods
179316 17602 14119 226
Neutron Other Total
77 37 211377
round(totals/totals["Total"]*100, 2)
X.ray EM NMR Multiple.methods
84.83 8.33 6.68 0.11
Neutron Other Total
0.04 0.02 100.00
84.83 + 8.33
[1] 93.16
Q1: What percentage of structures in the PDB are solved by X-ray and Electron Microscopy? - 93.16%
Q2: What proportion of structures in the PDB are protein? - SKIP
Q3: Type HIV in the PDB website search box on the homepage and determine how many HIV-1 protease structures are in the current PDB? - SKIP
#less ~/Downloads/1hsg.pdb
Here is a rubbish pic of HIV-Pr that is not very useful… yet!
Q4: Water molecules normally have 3 atoms.
Why do we see just one atom per water molecule in this structure? -
because the resolution is not high enough to resolve the water molecule.
the resolution of this structure 2Å.
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 - HOH308
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
attributes(pdb$helix)
$names
[1] "start" "end" "chain" "type"
head(pdb$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>
head(pdb$atom$resid)
[1] "PRO" "PRO" "PRO" "PRO" "PRO" "PRO"
aa321(pdb$atom$resid[pdb$calpha])
[1] "P" "Q" "I" "T" "L" "W" "Q" "R" "P" "L" "V" "T" "I" "K" "I" "G" "G" "Q"
[19] "L" "K" "E" "A" "L" "L" "D" "T" "G" "A" "D" "D" "T" "V" "L" "E" "E" "M"
[37] "S" "L" "P" "G" "R" "W" "K" "P" "K" "M" "I" "G" "G" "I" "G" "G" "F" "I"
[55] "K" "V" "R" "Q" "Y" "D" "Q" "I" "L" "I" "E" "I" "C" "G" "H" "K" "A" "I"
[73] "G" "T" "V" "L" "V" "G" "P" "T" "P" "V" "N" "I" "I" "G" "R" "N" "L" "L"
[91] "T" "Q" "I" "G" "C" "T" "L" "N" "F" "P" "Q" "I" "T" "L" "W" "Q" "R" "P"
[109] "L" "V" "T" "I" "K" "I" "G" "G" "Q" "L" "K" "E" "A" "L" "L" "D" "T" "G"
[127] "A" "D" "D" "T" "V" "L" "E" "E" "M" "S" "L" "P" "G" "R" "W" "K" "P" "K"
[145] "M" "I" "G" "G" "I" "G" "G" "F" "I" "K" "V" "R" "Q" "Y" "D" "Q" "I" "L"
[163] "I" "E" "I" "C" "G" "H" "K" "A" "I" "G" "T" "V" "L" "V" "G" "P" "T" "P"
[181] "V" "N" "I" "I" "G" "R" "N" "L" "L" "T" "Q" "I" "G" "C" "T" "L" "N" "F"
Run a Normal Mode Analysis (NMA)
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
modes <- nma(adk)
Building Hessian... Done in 0.013 seconds.
Diagonalizing Hessian... Done in 0.299 seconds.
plot(modes)
mktrj(modes, pdb=adk, file="modes.pdb")
Q7: How many amino acid residues are there in this pdb object? - 198
Q8: Name one of the two non-protein residues? - HOH127
Q9: How many protein chains are in this structure? - 2 chains: A, B