SMTL ID : 2dxd.1 (1 other biounit)

Crystal structure of nucleoside diphosphate kinase in complex with ATP analog

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

homo-hexamer

Ligands

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 4 residues within 4Å: Chain A: G.95, A.96, A.102, A.103 Ligand excluded by PLIP CL.3: 4 residues within 4Å: Chain B: G.95, A.96, A.102, A.103 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain C: G.95, A.96, A.102, A.103 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain D: G.95, A.96, A.102, A.103 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain E: G.95, A.96, A.102, A.103 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain F: G.95, A.96, A.102, A.103 Ligand excluded by PLIP

6 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.2: 8 residues within 4Å: Chain A: K.15, H.58, F.63, L.67, T.97, R.108, I.119, N.121 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:K.15, A:K.15, A:R.108, A:N.121 Water bridges: A:Y.55, A:R.91, A:R.91, A:R.91, A:H.124 Salt bridges: A:H.58 pi-Stacking: A:F.63, A:F.63 AMP.4: 10 residues within 4Å: Chain B: K.15, Y.55, H.58, F.63, L.67, T.97, R.108, A.118, I.119, N.121 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:K.15, B:K.15, B:E.57, B:R.108, B:I.119, B:N.121 Water bridges: B:H.124 Salt bridges: B:H.58 pi-Stacking: B:F.63, B:F.63 AMP.6: 8 residues within 4Å: Chain C: K.15, H.58, F.63, L.67, T.97, R.108, I.119, N.121 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:K.15, C:K.15, C:R.108, C:N.121 Water bridges: C:Y.55, C:R.91, C:R.91, C:R.91, C:H.124 Salt bridges: C:H.58 pi-Stacking: C:F.63, C:F.63 AMP.8: 10 residues within 4Å: Chain D: K.15, Y.55, H.58, F.63, L.67, T.97, R.108, A.118, I.119, N.121 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:K.15, D:K.15, D:E.57, D:R.108, D:I.119, D:N.121 Water bridges: D:H.124 Salt bridges: D:H.58 pi-Stacking: D:F.63, D:F.63 AMP.10: 8 residues within 4Å: Chain E: K.15, H.58, F.63, L.67, T.97, R.108, I.119, N.121 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:K.15, E:K.15, E:R.108, E:N.121 Water bridges: E:Y.55, E:R.91, E:R.91, E:R.91, E:H.124 Salt bridges: E:H.58 pi-Stacking: E:F.63, E:F.63 AMP.12: 10 residues within 4Å: Chain F: K.15, Y.55, H.58, F.63, L.67, T.97, R.108, A.118, I.119, N.121 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:K.15, F:K.15, F:E.57, F:R.108, F:I.119, F:N.121 Water bridges: F:H.124 Salt bridges: F:H.58 pi-Stacking: F:F.63, F:F.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kato-Murayama, M. et al., Crystal structure of nucleoside diphosphate kinase in complex with ATP analog. To be Published

Release Date

2007-02-25

Peptides

Nucleoside diphosphate kinase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Nucleoside diphosphate kinase

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