SMTL ID : 2hvd.1

Human nucleoside diphosphate kinase A complexed with ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-hexamer

Ligands

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

ADP.1: 10 residues within 4Å: Chain A: K.12, Y.52, L.55, F.60, L.64, R.88, T.94, V.112, G.113, N.115 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:K.12, A:N.115, A:N.115 Water bridges: A:R.88, A:G.119 Salt bridges: A:R.88, A:R.105 pi-Stacking: A:F.60, A:F.60 ADP.2: 11 residues within 4Å: Chain B: K.12, Y.52, L.55, F.60, L.64, R.88, T.94, R.105, V.112, G.113, N.115 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:K.12, B:R.105, B:N.115, B:N.115 Water bridges: B:K.12, B:R.88, B:R.88, B:R.88, B:R.105, B:R.105, B:G.119 Salt bridges: B:R.88 pi-Stacking: B:F.60 ADP.3: 11 residues within 4Å: Chain C: K.12, Y.52, L.55, F.60, L.64, R.88, T.94, R.105, V.112, G.113, N.115 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:K.12, C:Y.52, C:Y.52, C:T.94, C:R.105, C:N.115, C:N.115 Salt bridges: C:R.88, C:R.105 pi-Stacking: C:F.60, C:F.60 ADP.4: 10 residues within 4Å: Chain D: K.12, Y.52, L.55, F.60, L.64, R.88, T.94, V.112, G.113, N.115 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:K.12, D:T.94, D:N.115, D:N.115 Water bridges: D:R.88, D:R.105 Salt bridges: D:R.88, D:R.105 pi-Stacking: D:F.60, D:F.60 ADP.5: 11 residues within 4Å: Chain E: K.12, Y.52, L.55, F.60, L.64, R.88, T.94, R.105, V.112, G.113, N.115 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:K.12, E:T.94, E:R.105, E:N.115, E:N.115 Water bridges: E:K.12, E:R.88, E:R.88, E:R.88, E:R.105, E:R.105, E:H.118, E:G.119 Salt bridges: E:R.88 pi-Stacking: E:F.60 ADP.6: 11 residues within 4Å: Chain F: K.12, Y.52, L.55, F.60, L.64, R.88, T.94, R.105, V.112, G.113, N.115 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:K.12, F:Y.52, F:R.105, F:N.115, F:N.115 Salt bridges: F:R.88, F:R.105 pi-Stacking: F:F.60, F:F.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Giraud, M.-F. et al., Crystal Structures of S120G Mutant and Wild Type of Human Nucleoside Diphosphate Kinase A in Complex with ADP. J.Bioenerg.Biomembr. (2006)

Release Date

2006-09-19

Peptides

Nucleoside diphosphate kinase A: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Nucleoside diphosphate kinase A

Related Entries With Identical Sequence