SMTL ID : 1zs6.1

structure of human nucleoside-diphosphate kinase 3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-hexamer

Ligands

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

ADP.1: 10 residues within 4Å: Chain A: K.29, Y.69, L.72, F.77, L.81, R.105, T.111, R.122, V.129, N.132 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:K.29, A:T.111, A:R.122, A:N.132, A:N.132 Salt bridges: A:R.105, A:R.122 pi-Stacking: A:F.77, A:F.77 ADP.2: 11 residues within 4Å: Chain A: E.169 Chain B: K.29, Y.69, L.72, F.77, L.81, R.105, T.111, V.129, G.130, N.132 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:K.29, B:N.132, B:N.132 Water bridges: B:R.122, B:I.134 Salt bridges: B:R.105 pi-Stacking: B:F.77, B:F.77 ADP.3: 11 residues within 4Å: Chain C: K.29, Y.69, L.72, F.77, L.81, R.105, T.111, R.122, V.129, G.130, N.132 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:K.29, C:N.132, C:N.132 Water bridges: C:K.29, C:R.122, C:R.122 Salt bridges: C:R.105, C:R.122 pi-Stacking: C:F.77, C:F.77 ADP.4: 10 residues within 4Å: Chain D: K.29, Y.69, L.72, F.77, L.81, R.105, T.111, R.122, V.129, N.132 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:K.29, D:R.122, D:N.132, D:N.132 Salt bridges: D:R.105, D:R.122 pi-Stacking: D:F.77, D:F.77 ADP.5: 11 residues within 4Å: Chain D: E.169 Chain E: K.29, Y.69, L.72, F.77, L.81, R.105, T.111, V.129, G.130, N.132 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:K.29, E:T.111, E:N.132, E:N.132 Water bridges: E:R.122, E:I.134 Salt bridges: E:R.105 pi-Stacking: E:F.77, E:F.77 ADP.6: 11 residues within 4Å: Chain F: K.29, Y.69, L.72, F.77, L.81, R.105, T.111, R.122, V.129, G.130, N.132 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:K.29, F:T.111, F:N.132, F:N.132 Water bridges: F:K.29, F:R.122, F:R.122, F:H.135 Salt bridges: F:R.105, F:R.122 pi-Stacking: F:F.77, F:F.77

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dimov, S. et al., Structure of human nucleoside-diphosphate kinase 3. To be Published

Release Date

2005-06-07

Peptides

Nucleoside diphosphate kinase 3: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
A

E
B

F
D

Nucleoside diphosphate kinase 3