Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

1g6o

2.500 Å

X-ray

2000-11-07

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Cag alpha
ID:Q7BK04_HELPX
AC:Q7BK04
Organism:Helicobacter pylori
Reign:Bacteria
TaxID:210
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A3 %
B97 %


Ligand binding site composition:

B-Factor:31.679
Number of residues:33
Including
Standard Amino Acids: 32
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.4062035.125

% Hydrophobic% Polar
37.8162.19
According to VolSite

Ligand :
1g6o_2 Structure
HET Code: ADP
Formula: C10H12N5O10P2
Molecular weight: 424.177 g/mol
DrugBank ID: -
Buried Surface Area:56.56 %
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
-12.49423.621121.5836


Binding mode :
What is Poseview ?
  • 2D View
  • 3D View
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
O2BNH2ARG- 1333.05127.33H-Bond
(Protein Donor)
O2BNGLY- 1812.73146.93H-Bond
(Protein Donor)
O1BNGLY- 1833.2146.68H-Bond
(Protein Donor)
O3ANGLY- 1833.21129.87H-Bond
(Protein Donor)
O1BNZLYS- 1842.9158.84H-Bond
(Protein Donor)
O1BNLYS- 1843.06146.11H-Bond
(Protein Donor)
O1BNZLYS- 1842.90Ionic
(Protein Cationic)
O3BOG1THR- 1852.73175.94H-Bond
(Protein Donor)
O2AOG1THR- 1862.66162.92H-Bond
(Protein Donor)
O2ANTHR- 1862.75154.09H-Bond
(Protein Donor)
O3'OHOH- 12862.62179.98H-Bond
(Protein Donor)