SMTL ID : 3q8y.2 (7 other biounits)

Crystal structure of Staphylococcus aureus nucleoside diphosphate kinase complexed with ADP and Vanadate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

monomer

Ligands

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 9 residues within 4Å: Chain A: E.51, H.52, F.57, T.91, V.109, G.110, D.118 Ligands: VO4.2, MG.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.118 Water bridges: A:E.51, A:E.51, A:D.118 Salt bridges: A:H.52, A:H.52 pi-Stacking: A:F.57, A:F.57

1 x VO4: VANADATE ION(Non-covalent)

VO4.2: 6 residues within 4Å: Chain A: K.9, Y.49, R.102, H.115, G.116 Ligands: ADP.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.9, A:K.9, A:R.102, A:R.102, A:G.116

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.3: 1 residues within 4Å: Ligands: ADP.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Srivastava, S.K. et al., Conformational basis for substrate recognition and regulation of catalytic activity in Staphylococcus aureus nucleoside di-phosphate kinase. Biochim.Biophys.Acta (2011)

Release Date

2011-07-27

Peptides

Nucleoside diphosphate kinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Nucleoside diphosphate kinase

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