SMTL ID : 3q8u.1 (1 other biounit)

Crystal structure of Staphylococcus aureus nucleoside diphosphate kinase complexed with ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.22 Å

Oligo State

homo-trimer

Ligands

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

ADP.1: 11 residues within 4Å: Chain A: K.9, Y.49, H.52, F.57, L.61, T.91, R.102, V.109, G.110, N.112 Ligands: MG.2 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:K.9, A:T.91, A:R.102, A:N.112, A:N.112 Water bridges: A:K.9, A:K.55, A:R.85, A:D.118, A:D.118, A:D.118 Salt bridges: A:H.52, A:R.102 pi-Stacking: A:F.57, A:F.57 ADP.3: 11 residues within 4Å: Chain B: K.9, Y.49, H.52, F.57, L.61, T.91, R.102, V.109, G.110, N.112 Ligands: MG.4 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:K.9, B:R.102, B:N.112, B:N.112 Water bridges: B:K.9, B:Y.49, B:R.102, B:R.102, B:R.102, B:D.118, B:D.118, B:D.118 Salt bridges: B:H.52, B:R.102 pi-Stacking: B:F.57, B:F.57 ADP.5: 12 residues within 4Å: Chain A: E.149 Chain C: K.9, Y.49, H.52, F.57, L.61, T.91, R.102, V.109, G.110, N.112 Ligands: MG.6 15 PLIP interactions: 1 interactions with chain A, 14 interactions with chain C Water bridges: A:E.149, C:K.9, C:Y.49, C:R.85, C:R.85, C:G.116 Hydrogen bonds: C:K.9, C:T.91, C:R.102, C:N.112, C:N.112 Salt bridges: C:H.52, C:R.102 pi-Stacking: C:F.57, C:F.57

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: E.51, D.118 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain B: D.118 Ligands: ADP.3 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.118, H2O.4, H2O.4, H2O.7 MG.6: 2 residues within 4Å: Chain C: D.118 Ligands: ADP.5 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.118, H2O.7, H2O.7, H2O.7

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: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
E

Nucleoside diphosphate kinase

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