SMTL ID : 1be4.1

NUCLEOSIDE DIPHOSPHATE KINASE ISOFORM B FROM BOVINE RETINA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-hexamer

Ligands

6 x PCG: CYCLIC GUANOSINE MONOPHOSPHATE(Non-covalent)

PCG.1: 10 residues within 4Å: Chain A: K.11, Y.51, F.59, L.63, T.93, V.111, G.112, N.114, H.117 Chain B: E.151 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.11, A:Y.51, A:N.114, A:N.114, B:E.151 Salt bridges: A:K.11, A:H.117 pi-Stacking: A:F.59, A:F.59 pi-Cation interactions: A:F.59 PCG.2: 11 residues within 4Å: Chain B: K.11, Y.51, F.59, R.87, T.93, R.104, V.111, G.112, N.114, H.117 Chain C: E.151 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Y.51, B:R.87, B:R.104, B:N.114, B:N.114, C:E.151 Water bridges: B:Y.51, B:H.117 Salt bridges: B:K.11, B:H.117 pi-Stacking: B:F.59, B:F.59 PCG.3: 11 residues within 4Å: Chain A: E.151 Chain C: K.11, Y.51, L.54, F.59, L.63, T.93, R.104, V.111, N.114, H.117 13 PLIP interactions: 12 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Y.51, C:Y.51, C:N.114, C:N.114 Water bridges: C:R.87, C:R.87, C:G.112 Salt bridges: C:K.11, C:R.104, C:H.117, A:E.151 pi-Stacking: C:F.59, C:F.59 PCG.4: 10 residues within 4Å: Chain D: K.11, Y.51, F.59, L.63, T.93, V.111, G.112, N.114, H.117 Chain E: E.151 11 PLIP interactions: 10 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:K.11, D:N.114, D:N.114, E:E.151 Water bridges: D:H.117, D:H.117 Salt bridges: D:K.11, D:H.117 pi-Stacking: D:F.59, D:F.59 pi-Cation interactions: D:F.59 PCG.5: 11 residues within 4Å: Chain E: K.11, Y.51, F.59, R.87, T.93, R.104, V.111, G.112, N.114, H.117 Chain F: E.151 10 PLIP interactions: 9 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:R.87, E:R.104, E:N.114, F:E.151 Water bridges: E:Y.51, E:H.117 Salt bridges: E:K.11, E:H.117 pi-Stacking: E:F.59, E:F.59 PCG.6: 11 residues within 4Å: Chain D: E.151 Chain F: K.11, Y.51, L.54, F.59, L.63, T.93, R.104, V.111, N.114, H.117 13 PLIP interactions: 12 interactions with chain F, 1 interactions with chain D Hydrogen bonds: F:Y.51, F:N.114, F:N.114 Water bridges: F:R.87, F:R.87, F:G.112, F:H.117 Salt bridges: F:K.11, F:R.104, F:H.117, D:E.151 pi-Stacking: F:F.59, F:F.59

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abdulaev, N.G. et al., Nucleoside diphosphate kinase from bovine retina: purification, subcellular localization, molecular cloning, and three-dimensional structure. Biochemistry (1998)

Release Date

1999-01-13

Peptides

NUCLEOSIDE DIPHOSPHATE TRANSFERASE: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

NUCLEOSIDE DIPHOSPHATE TRANSFERASE