SMTL ID : 1wkk.1

Crystal Structure of Nucleoside Diphosphate Kinase from Thermus thermophilus HB8 in Complex with GDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-hexamer

Ligands

3 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.1: 13 residues within 4Å: Chain A: K.9, Y.49, H.52, F.57, L.61, R.85, T.91, R.102, I.109, D.110, N.112, I.114, H.115 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:K.9, A:K.9, A:Y.49, A:Y.49, A:R.85, A:T.91, A:T.91, A:I.109, A:N.112 Water bridges: A:R.102, A:H.115, A:G.116 Salt bridges: A:K.9, A:R.102, A:D.110, A:H.115, A:H.115 pi-Stacking: A:F.57, A:F.57 GDP.2: 13 residues within 4Å: Chain C: K.9, Y.49, H.52, F.57, L.61, R.85, T.91, R.102, I.109, D.110, N.112, I.114, H.115 19 PLIP interactions: 19 interactions with chain C Hydrogen bonds: C:K.9, C:K.9, C:Y.49, C:Y.49, C:R.85, C:T.91, C:T.91, C:I.109, C:N.112 Water bridges: C:R.102, C:H.115, C:G.116 Salt bridges: C:K.9, C:R.102, C:D.110, C:H.115, C:H.115 pi-Stacking: C:F.57, C:F.57 GDP.3: 13 residues within 4Å: Chain E: K.9, Y.49, H.52, F.57, L.61, R.85, T.91, R.102, I.109, D.110, N.112, I.114, H.115 19 PLIP interactions: 19 interactions with chain E Hydrogen bonds: E:K.9, E:K.9, E:Y.49, E:Y.49, E:R.85, E:T.91, E:T.91, E:I.109, E:N.112 Water bridges: E:R.102, E:H.115, E:G.116 Salt bridges: E:K.9, E:R.102, E:D.110, E:H.115, E:H.115 pi-Stacking: E:F.57, E:F.57

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Takeishi, S. et al., Crystal Structure of Nucleoside Diphosphate Kinase from Thermus thermophilus HB8. To be Published

Release Date

2005-08-23

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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