SMTL ID : 2dy9.1

Crystal structure of nucleoside diphosphate kinase in complex with ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

homo-hexamer

Ligands

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

MG.1: 1 residues within 4Å: Ligands: ADP.4 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Ligands: ADP.10 No protein-ligand interaction detected (PLIP) MG.13: 1 residues within 4Å: Ligands: ADP.16 No protein-ligand interaction detected (PLIP)

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

CL.2: 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 A: R.150, A.151, A.152 Chain B: V.20 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain B: G.95, A.96, A.102, A.103 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: V.20 Chain B: R.150, A.151, A.152 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain C: G.95, A.96, A.102, A.103 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain C: R.150, A.151, A.152 Chain D: V.20 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain D: G.95, A.96, A.102, A.103 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain C: V.20 Chain D: R.150, A.151, A.152 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain E: G.95, A.96, A.102, A.103 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain E: R.150, A.151, A.152 Chain F: V.20 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain F: G.95, A.96, A.102, A.103 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain E: V.20 Chain F: R.150, A.151, A.152 Ligand excluded by PLIP

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

ADP.4: 12 residues within 4Å: Chain A: K.15, Y.55, H.58, F.63, L.67, Y.70, R.91, T.97, R.108, I.119, N.121 Ligands: MG.1 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:K.15, A:T.97, A:I.119, A:N.121, A:N.121 Water bridges: A:K.15, A:Y.55, A:R.91, A:R.91, A:R.91, A:R.91, A:R.108, A:H.124 Salt bridges: A:H.58, A:R.91, A:R.108 pi-Stacking: A:F.63, A:F.63 ADP.10: 12 residues within 4Å: Chain C: K.15, Y.55, H.58, F.63, L.67, Y.70, R.91, T.97, R.108, I.119, N.121 Ligands: MG.7 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:K.15, C:T.97, C:I.119, C:N.121, C:N.121 Water bridges: C:K.15, C:Y.55, C:R.91, C:R.91, C:R.91, C:R.91, C:R.108, C:H.124 Salt bridges: C:H.58, C:R.91, C:R.108 pi-Stacking: C:F.63, C:F.63 ADP.16: 12 residues within 4Å: Chain E: K.15, Y.55, H.58, F.63, L.67, Y.70, R.91, T.97, R.108, I.119, N.121 Ligands: MG.13 18 PLIP interactions: 18 interactions with chain E Hydrogen bonds: E:K.15, E:T.97, E:I.119, E:N.121, E:N.121 Water bridges: E:K.15, E:Y.55, E:R.91, E:R.91, E:R.91, E:R.91, E:R.108, E:H.124 Salt bridges: E:H.58, E:R.91, E:R.108 pi-Stacking: E:F.63, E: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 ADP. To be Published

Release Date

2007-03-08

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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