SMTL ID : 3b54.1

Saccharomyces cerevisiae nucleoside diphosphate kinase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-hexamer

Ligands

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 7 residues within 4Å: Chain A: Y.61, R.97, T.103, R.114, N.124, H.127, G.128 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.61, A:R.114, A:N.124, A:G.128, A:G.128 Salt bridges: A:K.21, A:R.97, A:H.127 PO4.2: 8 residues within 4Å: Chain B: K.21, Y.61, R.97, T.103, R.114, N.124, H.127, G.128 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Y.61, B:R.114, B:N.124, B:G.128, B:G.128 Salt bridges: B:K.21, B:R.97, B:H.127 PO4.3: 7 residues within 4Å: Chain C: Y.61, R.97, T.103, R.114, N.124, H.127, G.128 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:R.114, C:N.124, C:G.128, C:G.128 Salt bridges: C:K.21, C:R.97, C:H.127 PO4.4: 8 residues within 4Å: Chain D: K.21, Y.61, R.97, T.103, R.114, N.124, H.127, G.128 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:R.114, D:N.124, D:G.128, D:G.128 Salt bridges: D:K.21, D:R.97, D:H.127 PO4.5: 7 residues within 4Å: Chain E: Y.61, R.97, T.103, R.114, N.124, H.127, G.128 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:Y.61, E:R.114, E:N.124, E:G.128, E:G.128 Salt bridges: E:K.21, E:R.97, E:H.127 PO4.6: 8 residues within 4Å: Chain F: K.21, Y.61, R.97, T.103, R.114, N.124, H.127, G.128 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:R.114, F:N.124, F:G.128, F:G.128 Salt bridges: F:K.21, F:R.97, F:H.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, H. et al., Structure of Ynk1 from the yeast Saccharomyces cerevisiae. Acta Crystallogr.,Sect.F (2008)

Release Date

2008-10-07

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