SMTL ID : 2dxd.2 (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-12-mer

Ligands

12 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 CL.13: 4 residues within 4Å: Chain G: G.95, A.96, A.102, A.103 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain H: G.95, A.96, A.102, A.103 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain I: G.95, A.96, A.102, A.103 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain J: G.95, A.96, A.102, A.103 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain K: G.95, A.96, A.102, A.103 Ligand excluded by PLIP CL.23: 4 residues within 4Å: Chain L: G.95, A.96, A.102, A.103 Ligand excluded by PLIP

12 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.2: 9 residues within 4Å: Chain A: K.15, H.58, F.63, L.67, T.97, R.108, I.119, N.121 Ligands: AMP.22 13 PLIP interactions: 13 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:T.97, 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: 9 residues within 4Å: Chain C: K.15, H.58, F.63, L.67, T.97, R.108, I.119, N.121 Ligands: AMP.18 13 PLIP interactions: 13 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:T.97, 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: 9 residues within 4Å: Chain E: K.15, H.58, F.63, L.67, T.97, R.108, I.119, N.121 Ligands: AMP.14 13 PLIP interactions: 13 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:T.97, 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 AMP.14: 9 residues within 4Å: Chain G: K.15, H.58, F.63, L.67, T.97, R.108, I.119, N.121 Ligands: AMP.10 11 PLIP interactions: 11 interactions with chain G Hydrogen bonds: G:K.15, G:K.15, G:R.108, G:N.121 Water bridges: G:R.91, G:R.91, G:H.124, G:D.127 Salt bridges: G:H.58 pi-Stacking: G:F.63, G:F.63 AMP.16: 10 residues within 4Å: Chain H: K.15, Y.55, H.58, F.63, L.67, T.97, R.108, A.118, I.119, N.121 11 PLIP interactions: 11 interactions with chain H Hydrogen bonds: H:K.15, H:K.15, H:Y.55, H:T.97, H:R.108, H:I.119, H:N.121 Water bridges: H:H.124 Salt bridges: H:H.58 pi-Stacking: H:F.63, H:F.63 AMP.18: 9 residues within 4Å: Chain I: K.15, H.58, F.63, L.67, T.97, R.108, I.119, N.121 Ligands: AMP.6 11 PLIP interactions: 11 interactions with chain I Hydrogen bonds: I:K.15, I:K.15, I:R.108, I:N.121 Water bridges: I:R.91, I:R.91, I:H.124, I:D.127 Salt bridges: I:H.58 pi-Stacking: I:F.63, I:F.63 AMP.20: 10 residues within 4Å: Chain J: K.15, Y.55, H.58, F.63, L.67, T.97, R.108, A.118, I.119, N.121 11 PLIP interactions: 11 interactions with chain J Hydrogen bonds: J:K.15, J:K.15, J:Y.55, J:T.97, J:R.108, J:I.119, J:N.121 Water bridges: J:H.124 Salt bridges: J:H.58 pi-Stacking: J:F.63, J:F.63 AMP.22: 9 residues within 4Å: Chain K: K.15, H.58, F.63, L.67, T.97, R.108, I.119, N.121 Ligands: AMP.2 11 PLIP interactions: 11 interactions with chain K Hydrogen bonds: K:K.15, K:K.15, K:R.108, K:N.121 Water bridges: K:R.91, K:R.91, K:H.124, K:D.127 Salt bridges: K:H.58 pi-Stacking: K:F.63, K:F.63 AMP.24: 10 residues within 4Å: Chain L: K.15, Y.55, H.58, F.63, L.67, T.97, R.108, A.118, I.119, N.121 11 PLIP interactions: 11 interactions with chain L Hydrogen bonds: L:K.15, L:K.15, L:Y.55, L:T.97, L:R.108, L:I.119, L:N.121 Water bridges: L:H.124 Salt bridges: L:H.58 pi-Stacking: L:F.63, L: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: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

I
A

J
B

K
A

L
B

Nucleoside diphosphate kinase

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