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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:

4b0j

2.500 Å

X-ray

2012-07-02

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
ID:FABA_PSEAE
AC:O33877
Organism:Pseudomonas aeruginosa
Reign:Bacteria
TaxID:208964
EC Number:4.2.1.59


Chains:

Chain Name:Percentage of Residues
within binding site
K5 %
O59 %
P36 %


Ligand binding site composition:

B-Factor:52.530
Number of residues:24
Including
Standard Amino Acids: 23
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.065880.875

% Hydrophobic% Polar
56.7043.30
According to VolSite

Ligand :
4b0j_13 Structure
HET Code: 3MQ
Formula: C8H7NO2S
Molecular weight: 181.212 g/mol
DrugBank ID: -
Buried Surface Area:72.15 %
Polar Surface area: 74.5 Å2
Number of
H-Bond Acceptors: 2
H-Bond Donors: 1
Rings: 2
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
5.2768318.8637208.043


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
C06CBALA- 1054.440Hydrophobic
C06CD2PHE- 1134.420Hydrophobic
S09CGGLN- 1163.830Hydrophobic
N04OHOH- 20273.26179.98H-Bond
(Protein Donor)