SMTL ID : 2az3.1 (1 other biounit)

Structure of a halophilic nucleoside diphosphate kinase from Halobacterium salinarum in complex with CDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: E.58, H.59 Ligands: CDP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.58 MG.3: 3 residues within 4Å: Chain B: E.58, H.59 Ligands: CDP.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.58 MG.6: 3 residues within 4Å: Chain D: E.58, H.59 Ligands: CDP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.58 MG.8: 3 residues within 4Å: Chain E: E.58, H.59 Ligands: CDP.9 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:E.58

6 x CDP: CYTIDINE-5'-DIPHOSPHATE(Non-covalent)

CDP.2: 12 residues within 4Å: Chain A: K.16, E.58, H.59, F.64, L.68, R.92, T.98, L.116, G.117, N.119, H.122 Ligands: MG.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.116 Hydrogen bonds: A:K.16, A:N.119, A:N.119 Water bridges: A:K.16, A:R.109, A:R.109, A:H.122 Salt bridges: A:H.59, A:R.92, A:H.122 pi-Stacking: A:F.64 CDP.4: 13 residues within 4Å: Chain B: K.16, Y.56, E.58, H.59, F.64, L.68, R.92, T.98, L.116, G.117, N.119, H.122 Ligands: MG.3 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.116 Hydrogen bonds: B:K.16, B:N.119, B:N.119, B:H.122 Water bridges: B:R.109 Salt bridges: B:H.59, B:R.92 pi-Stacking: B:F.64 CDP.5: 10 residues within 4Å: Chain C: K.16, H.59, F.64, L.68, R.92, T.98, L.116, G.117, N.119, H.122 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:K.16, C:N.119, C:N.119 Water bridges: C:R.92, C:R.109, C:H.122, C:H.122 Salt bridges: C:H.59, C:R.92, C:H.122 pi-Stacking: C:F.64 CDP.7: 12 residues within 4Å: Chain D: K.16, E.58, H.59, F.64, L.68, R.92, T.98, L.116, G.117, N.119, H.122 Ligands: MG.6 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:L.116 Hydrogen bonds: D:K.16, D:T.98, D:N.119, D:N.119 Water bridges: D:K.16, D:Y.56, D:R.109, D:R.109 Salt bridges: D:H.59, D:R.92, D:H.122 pi-Stacking: D:F.64 CDP.9: 13 residues within 4Å: Chain E: K.16, Y.56, E.58, H.59, F.64, L.68, R.92, T.98, L.116, G.117, N.119, H.122 Ligands: MG.8 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:L.116 Hydrogen bonds: E:K.16, E:T.98, E:N.119, E:N.119 Water bridges: E:R.109 Salt bridges: E:H.59, E:R.92 pi-Stacking: E:F.64 CDP.10: 10 residues within 4Å: Chain F: K.16, H.59, F.64, L.68, R.92, T.98, L.116, G.117, N.119, H.122 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:K.16, F:N.119, F:N.119 Water bridges: F:K.16, F:R.92, F:R.109, F:H.122 Salt bridges: F:H.59, F:R.92, F:H.122 pi-Stacking: F:F.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Besir, H. et al., Structure of a halophilic nucleoside diphosphate kinase from Halobacterium salinarum. Febs Lett. (2005)

Release Date

2005-12-20

Peptides

Nucleoside diphosphate kinase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Nucleoside diphosphate kinase

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