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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

3vmm

2.500 Å

X-ray

2011-12-14

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Alanine--anticapsin ligase
ID:BACD_BACSU
AC:P39641
Organism:Bacillus subtilis
Reign:Bacteria
TaxID:224308
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:34.444
Number of residues:37
Including
Standard Amino Acids: 32
Non Standard Amino Acids: 3
Water Molecules: 2
Cofactors: ADP
Metals: MG MG

Cavity properties

LigandabilityVolume (Å3)
1.2191316.250

% Hydrophobic% Polar
36.9263.08
According to VolSite

Ligand :
3vmm_1 Structure
HET Code: P0D
Formula: C12H17NO7P2
Molecular weight: 349.213 g/mol
DrugBank ID: -
Buried Surface Area:69.25 %
Polar Surface area: 176.88 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 1
Rings: 1
Aromatic rings: 1
Anionic atoms: 3
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 8

Mass center Coordinates

XYZ
-0.370591-47.1757-8.14227


Binding mode :
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Binding mode
BioSolveIT Image generated by PoseView
Protein
Binding Site
Ligand
Interaction pattern
hydrophobic (CA)
aromatic (CZ)
hydrogen bond acceptor (O)
hydrogen bond acceptor/donor (OG)
hydrogen bond donor (N)
positively ionized (NZ)
negatively ionized (OD1)
metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
C34CBLEU- 123.680Hydrophobic
O1NGLY- 142.84155.18H-Bond
(Protein Donor)
C35CBGLU- 1094.080Hydrophobic
C33CBALA- 1833.990Hydrophobic
O4PNSER- 1842.71142.34H-Bond
(Protein Donor)
C3'CBSER- 1844.170Hydrophobic
N1OE1GLU- 2732.96126.92H-Bond
(Ligand Donor)
N1OE1GLU- 2732.960Ionic
(Ligand Cationic)
N1NE2HIS- 3092.94162.15H-Bond
(Ligand Donor)
N1OE2GLU- 3112.970Ionic
(Ligand Cationic)
O1CZARG- 3283.970Ionic
(Protein Cationic)
O1PNH1ARG- 3283.39156.48H-Bond
(Protein Donor)
O2PNH2ARG- 3283.11159.81H-Bond
(Protein Donor)
O1PNGLY- 3312.92152.17H-Bond
(Protein Donor)
C2CEMET- 3343.730Hydrophobic
O5PMG MG- 5012.030Metal Acceptor
O1OHOH- 6502.72179.99H-Bond
(Protein Donor)
N1OHOH- 6563.21138.15H-Bond
(Ligand Donor)