Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

3dhb

1.400 Å

X-ray

2008-06-17

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:N-acyl homoserine lactonase AiiA
ID:AHLLA_BACTK
AC:P0CJ63
Organism:Bacillus thuringiensis subsp. kurstaki
Reign:Bacteria
TaxID:29339
EC Number:3.1.1.81


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:15.076
Number of residues:29
Including
Standard Amino Acids: 25
Non Standard Amino Acids: 2
Water Molecules: 2
Cofactors:
Metals: ZN ZN

Cavity properties

LigandabilityVolume (Å3)
1.213577.125

% Hydrophobic% Polar
54.9745.03
According to VolSite

Ligand :
3dhb_1 Structure
HET Code: C6L
Formula: C10H18NO4
Molecular weight: 216.254 g/mol
DrugBank ID: DB07532
Buried Surface Area:63.17 %
Polar Surface area: 89.46 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 2
Rings: 0
Aromatic rings: 0
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 8

Mass center Coordinates

XYZ
-16.1785-5.9757313.9116


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
C1SGCYS- 143.80Hydrophobic
C2CD1LEU- 163.510Hydrophobic
C1CGLEU- 163.590Hydrophobic
C1CE2PHE- 1074.330Hydrophobic
O3OD1ASP- 1082.7121.02H-Bond
(Ligand Donor)
C9CBALA- 2064.20Hydrophobic
C10CBPHE- 2084.350Hydrophobic
O2ZN ZN- 2512.060Metal Acceptor
O1ZN ZN- 2522.020Metal Acceptor
O4OHOH- 4112.68133.23H-Bond
(Protein Donor)