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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:

4bga

2.600 Å

X-ray

2013-03-24

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Predicted molecular chaperone distantly related to HSP70-fold metalloproteases
ID:Q8TX37_METKA
AC:Q8TX37
Organism:Methanopyrus kandleri
Reign:Archaea
TaxID:190192
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A96 %
C4 %


Ligand binding site composition:

B-Factor:29.383
Number of residues:29
Including
Standard Amino Acids: 28
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.643999.000

% Hydrophobic% Polar
32.0967.91
According to VolSite

Ligand :
4bga_1 Structure
HET Code: ADP
Formula: C10H12N5O10P2
Molecular weight: 424.177 g/mol
DrugBank ID: -
Buried Surface Area:49.06 %
Polar Surface area: 260.7 Å2
Number of
H-Bond Acceptors: 14
H-Bond Donors: 3
Rings: 3
Aromatic rings: 2
Anionic atoms: 3
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 6

Mass center Coordinates

XYZ
-1.8463-6.4967422.769


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
O1BOG1THR- 482.98138H-Bond
(Protein Donor)
C2'CBTHR- 1914.480Hydrophobic
C4'CBTHR- 1914.50Hydrophobic
O3'OG1THR- 1913.12163.91H-Bond
(Ligand Donor)
O2'OD1ASP- 1952.72164.6H-Bond
(Ligand Donor)
C2'CBTYR- 2063.770Hydrophobic
C3'CD2TYR- 2064.320Hydrophobic
N6OE2GLU- 2083.43160.1H-Bond
(Ligand Donor)
N1NGLY- 2092.87161.95H-Bond
(Protein Donor)
O1ANGLY- 2983.44156.8H-Bond
(Protein Donor)