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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:

3wrb

2.100 Å

X-ray

2014-02-21

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Gallate dioxygenase
ID:G2IKE5_9SPHN
AC:G2IKE5
Organism:Sphingobium sp. SYK-6
Reign:Bacteria
TaxID:627192
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A29 %
B71 %


Ligand binding site composition:

B-Factor:15.454
Number of residues:24
Including
Standard Amino Acids: 20
Non Standard Amino Acids: 1
Water Molecules: 3
Cofactors:
Metals: FE2

Cavity properties

LigandabilityVolume (Å3)
0.663273.375

% Hydrophobic% Polar
58.0241.98
According to VolSite

Ligand :
3wrb_1 Structure
HET Code: GDE
Formula: C7H5O5
Molecular weight: 169.112 g/mol
DrugBank ID: -
Buried Surface Area:71.55 %
Polar Surface area: 100.82 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 3
Rings: 1
Aromatic rings: 1
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 1

Mass center Coordinates

XYZ
23.00583.226429.17433


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
CAJCBTHR- 133.970Hydrophobic
CAFCGPRO- 143.60Hydrophobic
CAGCG1VAL- 1943.920Hydrophobic
OADOG1THR- 2672.77173.62H-Bond
(Ligand Donor)
OACOE1GLU- 3773.12136.37H-Bond
(Ligand Donor)
OAAND2ASN- 3872.77156.5H-Bond
(Protein Donor)
OAAOHTYR- 3912.64170.65H-Bond
(Protein Donor)
OABOHOH- 8182.68179.99H-Bond
(Protein Donor)