SMTL ID : 1bhn.1

NUCLEOSIDE DIPHOSPHATE KINASE ISOFORM A FROM BOVINE RETINA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-hexamer

Ligands

6 x 35G: GUANOSINE-3',5'-MONOPHOSPHATE(Non-covalent)

35G.1: 11 residues within 4Å: Chain A: K.12, Y.52, F.60, T.94, R.105, V.112, G.113, N.115, H.118 Chain B: E.152 Ligands: GDP.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.105, A:N.115 Salt bridges: A:K.12, A:H.118 pi-Stacking: A:F.60, A:F.60 35G.3: 14 residues within 4Å: Chain B: K.12, Y.52, L.55, F.60, T.94, R.105, V.112, G.113, N.115, I.117, H.118, G.119 Chain C: E.152 Ligands: GDP.4 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:K.12, B:Y.52, B:N.115, B:N.115, B:G.119 Salt bridges: B:K.12, B:R.105, B:H.118 pi-Stacking: B:F.60, B:F.60 35G.5: 11 residues within 4Å: Chain C: K.12, Y.52, L.55, F.60, L.64, T.94, R.105, V.112, N.115, H.118 Ligands: GDP.6 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:K.12, C:T.94, C:R.105, C:N.115 Water bridges: C:G.119, A:E.152 Salt bridges: C:K.12, C:H.118 pi-Stacking: C:F.60, C:F.60 35G.7: 11 residues within 4Å: Chain D: K.12, Y.52, L.55, F.60, L.64, R.105, V.112, G.113, N.115, H.118 Ligands: GDP.8 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:K.12, D:R.105, D:N.115 Water bridges: D:R.58 Salt bridges: D:K.12, D:H.118 pi-Stacking: D:F.60, D:F.60 35G.9: 10 residues within 4Å: Chain E: K.12, Y.52, F.60, T.94, V.112, G.113, N.115, H.118 Chain F: E.152 Ligands: GDP.10 10 PLIP interactions: 9 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:K.12, E:R.105, E:N.115, F:E.152 Water bridges: E:G.119, E:G.119 Salt bridges: E:K.12, E:H.118 pi-Stacking: E:F.60, E:F.60 35G.11: 12 residues within 4Å: Chain D: E.152 Chain F: K.12, Y.52, F.60, L.64, T.94, R.105, V.112, G.113, N.115, H.118 Ligands: GDP.12 9 PLIP interactions: 1 interactions with chain D, 8 interactions with chain F Hydrogen bonds: D:E.152, F:K.12, F:Y.52, F:R.105, F:N.115 Salt bridges: F:K.12, F:H.118 pi-Stacking: F:F.60, F:F.60

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

GDP.2: 11 residues within 4Å: Chain A: K.12, F.60, R.88, T.94, R.105, V.112, G.113, N.115, H.118 Chain B: E.152 Ligands: 35G.1 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.12, A:T.94, A:T.94, A:R.105, A:N.115, B:E.152 Water bridges: A:R.105, A:G.113, A:G.119 Salt bridges: A:R.88, A:H.118 pi-Stacking: A:F.60, A:F.60 GDP.4: 13 residues within 4Å: Chain B: K.12, Y.52, L.55, F.60, L.64, R.88, T.94, V.112, N.115, H.118, G.119 Chain C: E.152 Ligands: 35G.3 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:K.12, B:Y.52, B:N.115, B:N.115, B:G.119, C:E.152 Water bridges: B:R.88, B:R.88, B:T.94 Salt bridges: B:R.88, B:H.118 pi-Stacking: B:F.60, B:F.60 GDP.6: 13 residues within 4Å: Chain A: E.152 Chain C: K.12, Y.52, L.55, F.60, L.64, R.88, T.94, R.105, V.112, N.115, H.118 Ligands: 35G.5 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:K.12, C:T.94, C:R.105, C:N.115, C:H.118, A:E.152 Water bridges: C:R.88, C:G.119 Salt bridges: C:R.88 pi-Stacking: C:F.60, C:F.60 pi-Cation interactions: C:F.60 GDP.8: 12 residues within 4Å: Chain D: K.12, Y.52, L.55, F.60, L.64, R.88, T.94, R.105, V.112, N.115 Chain E: E.152 Ligands: 35G.7 12 PLIP interactions: 1 interactions with chain E, 11 interactions with chain D Hydrogen bonds: E:E.152, D:K.12, D:T.94, D:R.105, D:N.115 Water bridges: D:R.58, D:R.88, D:R.88 Salt bridges: D:R.88 pi-Stacking: D:F.60, D:F.60 pi-Cation interactions: D:F.60 GDP.10: 9 residues within 4Å: Chain E: K.12, F.60, L.64, R.88, T.94, V.112, N.115 Chain F: E.152 Ligands: 35G.9 11 PLIP interactions: 10 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:K.12, E:T.94, E:N.115, F:E.152 Water bridges: E:R.58, E:R.88, E:G.119, E:D.121 Salt bridges: E:R.88 pi-Stacking: E:F.60, E:F.60 GDP.12: 12 residues within 4Å: Chain D: E.152 Chain F: K.12, Y.52, L.55, F.60, L.64, R.88, T.94, V.112, N.115, H.118 Ligands: 35G.11 10 PLIP interactions: 1 interactions with chain D, 9 interactions with chain F Hydrogen bonds: D:E.152, F:K.12, F:R.105, F:N.115, F:H.118 Water bridges: F:R.88, F:R.88 Salt bridges: F:R.88 pi-Stacking: F:F.60, F:F.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ladner, J.E. et al., The three-dimensional structures of two isoforms of nucleoside diphosphate kinase from bovine retina. Acta Crystallogr.,Sect.D (1999)

Release Date

1999-02-16

Peptides

NUCLEOSIDE DIPHOSPHATE TRANSFERASE: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

NUCLEOSIDE DIPHOSPHATE TRANSFERASE