SMTL ID : 2dya.1

Crystal structure of complex between Adenine nucleotide and nucleoside diphosphate kinase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

homo-hexamer

Ligands

6 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.1: 1 residues within 4Å: Ligands: ADP.4 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain B: E.57 Ligands: ADP.8 No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Ligands: ADP.12 No protein-ligand interaction detected (PLIP) MG.13: 2 residues within 4Å: Chain D: E.57 Ligands: ADP.16 No protein-ligand interaction detected (PLIP) MG.17: 1 residues within 4Å: Ligands: ADP.20 No protein-ligand interaction detected (PLIP) MG.21: 2 residues within 4Å: Chain F: E.57 Ligands: ADP.24 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.6: 4 residues within 4Å: Chain B: G.95, A.96, A.102, A.103 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: V.20 Chain B: R.150, A.151, A.152 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain C: G.95, A.96, A.102, A.103 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain C: R.150, A.151, A.152 Chain D: V.20 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain D: G.95, A.96, A.102, A.103 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain C: V.20 Chain D: R.150, A.151, A.152 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain E: G.95, A.96, A.102, A.103 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain E: R.150, A.151, A.152 Chain F: V.20 Ligand excluded by PLIP CL.22: 4 residues within 4Å: Chain F: G.95, A.96, A.102, A.103 Ligand excluded by PLIP CL.23: 4 residues within 4Å: Chain E: V.20 Chain F: R.150, A.151, A.152 Ligand excluded by PLIP

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

ADP.4: 14 residues within 4Å: Chain A: K.15, Y.55, H.58, F.63, L.67, Y.70, R.91, T.97, R.108, D.117, A.118, I.119, N.121 Ligands: MG.1 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:K.15, A:T.97, A:R.108, 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.91, A:H.124 Salt bridges: A:H.58, A:R.91, A:R.108 pi-Stacking: A:F.63, A:F.63 ADP.8: 14 residues within 4Å: Chain B: K.15, Y.55, H.58, F.63, L.67, Y.70, R.91, T.97, R.108, D.117, A.118, I.119, N.121 Ligands: MG.5 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:K.15, B:I.119, B:N.121, B:N.121 Water bridges: B:K.15, B:R.91, B:R.91, B:T.97, B:R.108, B:R.108, B:H.124, B:D.127 Salt bridges: B:H.58, B:R.91, B:R.108 pi-Stacking: B:F.63, B:F.63 ADP.12: 14 residues within 4Å: Chain C: K.15, Y.55, H.58, F.63, L.67, Y.70, R.91, T.97, R.108, D.117, A.118, I.119, N.121 Ligands: MG.9 19 PLIP interactions: 19 interactions with chain C Hydrogen bonds: C:K.15, C:T.97, C:R.108, 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.91, C:H.124 Salt bridges: C:H.58, C:R.91, C:R.108 pi-Stacking: C:F.63, C:F.63 ADP.16: 14 residues within 4Å: Chain D: K.15, Y.55, H.58, F.63, L.67, Y.70, R.91, T.97, R.108, D.117, A.118, I.119, N.121 Ligands: MG.13 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:K.15, D:I.119, D:N.121, D:N.121 Water bridges: D:K.15, D:R.91, D:R.91, D:T.97, D:R.108, D:R.108, D:H.124, D:D.127 Salt bridges: D:H.58, D:R.91, D:R.108 pi-Stacking: D:F.63, D:F.63 ADP.20: 14 residues within 4Å: Chain E: K.15, Y.55, H.58, F.63, L.67, Y.70, R.91, T.97, R.108, D.117, A.118, I.119, N.121 Ligands: MG.17 19 PLIP interactions: 19 interactions with chain E Hydrogen bonds: E:K.15, E:T.97, E:R.108, 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.91, E:H.124 Salt bridges: E:H.58, E:R.91, E:R.108 pi-Stacking: E:F.63, E:F.63 ADP.24: 14 residues within 4Å: Chain F: K.15, Y.55, H.58, F.63, L.67, Y.70, R.91, T.97, R.108, D.117, A.118, I.119, N.121 Ligands: MG.21 17 PLIP interactions: 17 interactions with chain F Hydrogen bonds: F:K.15, F:I.119, F:N.121, F:N.121 Water bridges: F:K.15, F:R.91, F:R.91, F:T.97, F:R.108, F:R.108, F:H.124, F:D.127 Salt bridges: F:H.58, F:R.91, F:R.108 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 complex between Adenine nucleotide and nucleoside diphosphate kinase. 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

Related Entries With Identical Sequence