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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:

5ayj

2.050 Å

X-ray

2015-08-21

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Uric acid degradation bifunctional protein
ID:PUCL_BACSB
AC:Q45697
Organism:Bacillus sp.
Reign:Bacteria
TaxID:36824
EC Number:1.7.3.3


Chains:

Chain Name:Percentage of Residues
within binding site
A58 %
B42 %


Ligand binding site composition:

B-Factor:26.356
Number of residues:27
Including
Standard Amino Acids: 24
Non Standard Amino Acids: 0
Water Molecules: 3
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.112654.750

% Hydrophobic% Polar
34.0265.98
According to VolSite

Ligand :
5ayj_1 Structure
HET Code: MUA
Formula: C6H6N4O3
Molecular weight: 182.137 g/mol
DrugBank ID: DB03293
Buried Surface Area:76.79 %
Polar Surface area: 90.54 Å2
Number of
H-Bond Acceptors: 3
H-Bond Donors: 3
Rings: 2
Aromatic rings: 0
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 0

Mass center Coordinates

XYZ
14.576428.296168.9665


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
N7NTHR- 733.07166.02H-Bond
(Protein Donor)
N7OG1THR- 733.13127.1H-Bond
(Protein Donor)
O8OG1THR- 733.26163.96H-Bond
(Protein Donor)
O8NASP- 743.07154.02H-Bond
(Protein Donor)
C10CD2PHE- 1843.840Hydrophobic
C10CD2LEU- 1953.690Hydrophobic
O2NH2ARG- 2012.67156.45H-Bond
(Protein Donor)
O2NILE- 2492.6153.73H-Bond
(Protein Donor)
N1OE1GLN- 2502.84179.3H-Bond
(Ligand Donor)
O6NE2GLN- 2502.94161.06H-Bond
(Protein Donor)