Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

3zo7

2.220 Å

X-ray

2013-02-20

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Muconolactone Delta-isomerase
ID:Q8G9L0_RHOOP
AC:Q8G9L0
Organism:Rhodococcus opacus
Reign:Bacteria
TaxID:37919
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
H14 %
J86 %


Ligand binding site composition:

B-Factor:33.428
Number of residues:26
Including
Standard Amino Acids: 24
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors:
Metals: CL

Cavity properties

LigandabilityVolume (Å3)
0.878394.875

% Hydrophobic% Polar
68.3831.62
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median3zo7HydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802550Highcharts.com
Ligand :
3zo7_6 Structure
HET Code: K6H
Formula: C6H4ClO4
Molecular weight: 175.547 g/mol
DrugBank ID: -
Buried Surface Area:69.48 %
Polar Surface area: 66.43 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 0
Rings: 1
Aromatic rings: 0
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
41.635145.894437.7455
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median3zo7RingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation80510Highcharts.com


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
CLADCBMET- 74.360Hydrophobic
CLADCG2VAL- 93.560Hydrophobic
CAKCBALA- 274.070Hydrophobic
OACCZARG- 453.870Ionic
(Protein Cationic)
OACNH1ARG- 453.02152.08H-Bond
(Protein Donor)
OAAND2ASN- 522.9166.34H-Bond
(Protein Donor)
CLADCD2PHE- 734.340Hydrophobic
CAKCD2PHE- 733.420Hydrophobic
CLADCD2LEU- 773.880Hydrophobic
OAANE2HIS- 872.91153.17H-Bond
(Protein Donor)
OACNE2HIS- 873.48135.77H-Bond
(Protein Donor)