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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:

1sz3

1.600 Å

X-ray

2004-04-02

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:MutT/nudix family protein
ID:Q9RVK2_DEIRA
AC:Q9RVK2
Organism:Deinococcus radiodurans
Reign:Bacteria
TaxID:243230
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A81 %
B19 %


Ligand binding site composition:

B-Factor:24.381
Number of residues:32
Including
Standard Amino Acids: 31
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors:
Metals: MG

Cavity properties

LigandabilityVolume (Å3)
0.119405.000

% Hydrophobic% Polar
46.6753.33
According to VolSite

Ligand :
1sz3_1 Structure
HET Code: GNP
Formula: C10H13N6O13P3
Molecular weight: 518.164 g/mol
DrugBank ID: DB02082
Buried Surface Area:58.6 %
Polar Surface area: 338.36 Å2
Number of
H-Bond Acceptors: 16
H-Bond Donors: 5
Rings: 3
Aromatic rings: 1
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 8

Mass center Coordinates

XYZ
46.6611.1150927.5423


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
C3'CEMET- 13.870Hydrophobic
C4'CGGLU- 23.520Hydrophobic
C1'CBASP- 43.990Hydrophobic
O3'NH2ARG- 63.27164.42H-Bond
(Protein Donor)
O2BOGSER- 492.9135.84H-Bond
(Protein Donor)
DuArDuArPHE- 873.860Aromatic Face/Face
C2'CZPHE- 873.260Hydrophobic
O6OD2ASP- 892.87144.7H-Bond
(Protein Donor)
C3'CD1ILE- 933.680Hydrophobic
O1BNH1ARG- 952.93126.81H-Bond
(Protein Donor)