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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:

3nzp

3.000 Å

X-ray

2010-07-16

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Arginine decarboxylase
ID:Q0PAC6_CAMJE
AC:Q0PAC6
Organism:Campylobacter jejuni subsp. jejuni serotype O:2
Reign:Bacteria
TaxID:192222
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A7 %
B93 %


Ligand binding site composition:

B-Factor:41.590
Number of residues:27
Including
Standard Amino Acids: 27
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.080580.500

% Hydrophobic% Polar
40.7059.30
According to VolSite

Ligand :
3nzp_2 Structure
HET Code: PLP
Formula: C8H8NO6P
Molecular weight: 245.126 g/mol
DrugBank ID: DB00114
Buried Surface Area:78.71 %
Polar Surface area: 132.42 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 1
Rings: 1
Aromatic rings: 1
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 4

Mass center Coordinates

XYZ
-31.1905100.781-14.5817


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
C5CBPRO- 844.010Hydrophobic
C5ACGPRO- 843.630Hydrophobic
C4CGLYS- 864.430Hydrophobic
C4ACDLYS- 863.30Hydrophobic
C5ACG1VAL- 874.30Hydrophobic
C2ACBASN- 1324.220Hydrophobic
C2ACBHIS- 2334.210Hydrophobic
DuArDuArHIS- 2333.760Aromatic Face/Face
O3POGSER- 2362.91147.89H-Bond
(Protein Donor)
O1PNGLY- 2743.02152.63H-Bond
(Protein Donor)
N1OE1GLU- 3202.89141.94H-Bond
(Ligand Donor)
O2PNARG- 3232.74161.37H-Bond
(Protein Donor)
O3POHTYR- 5192.59152.31H-Bond
(Protein Donor)