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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:

2jjx

2.820 Å

X-ray

2008-04-23

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Uridylate kinase
ID:Q81S73_BACAN
AC:Q81S73
Organism:Bacillus anthracis
Reign:Bacteria
TaxID:1392
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A59 %
B32 %
C9 %


Ligand binding site composition:

B-Factor:97.019
Number of residues:22
Including
Standard Amino Acids: 19
Non Standard Amino Acids: 3
Water Molecules: 0
Cofactors: ATP ATP
Metals: MG

Cavity properties

LigandabilityVolume (Å3)
0.5141164.375

% Hydrophobic% Polar
34.4965.51
According to VolSite

Ligand :
2jjx_1 Structure
HET Code: ATP
Formula: C10H12N5O13P3
Molecular weight: 503.149 g/mol
DrugBank ID: DB00171
Buried Surface Area:48.91 %
Polar Surface area: 319.88 Å2
Number of
H-Bond Acceptors: 17
H-Bond Donors: 3
Rings: 3
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 8

Mass center Coordinates

XYZ
41.6195-26.2582112.979


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
O3GCZARG- 993.950Ionic
(Protein Cationic)
O1ACZARG- 992.90Ionic
(Protein Cationic)
O1ANH1ARG- 992.75124.57H-Bond
(Protein Donor)
O2ACZARG- 1173.840Ionic
(Protein Cationic)
O2ANH2ARG- 1172.7144.77H-Bond
(Protein Donor)
C4'CGARG- 1173.960Hydrophobic
O2GNE2HIS- 1202.56121.53H-Bond
(Protein Donor)