SMTL ID : 1nue.1

X-RAY STRUCTURE OF NM23 HUMAN NUCLEOSIDE DIPHOSPHATE KINASE B COMPLEXED WITH GDP AT 2 ANGSTROMS RESOLUTION

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-hexamer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 2 residues within 4Å: Chain A: D.120 Ligands: GDP.2 No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Ligands: GDP.5 No protein-ligand interaction detected (PLIP)

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

GDP.2: 13 residues within 4Å: Chain A: K.11, Y.51, L.54, F.59, L.63, R.87, T.93, R.104, V.111, G.112, N.114 Chain B: E.151 Ligands: MG.1 21 PLIP interactions: 18 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:K.11, A:T.93, A:N.114, A:N.114 Water bridges: A:K.11, A:Y.51, A:R.87, A:R.87, A:R.87, A:R.87, A:R.104, A:R.104, A:G.112, A:R.113, B:E.151, B:E.151 Salt bridges: A:R.87, A:R.104, B:E.151 pi-Stacking: A:F.59, A:F.59 GDP.3: 12 residues within 4Å: Chain B: K.11, Y.51, L.54, F.59, L.63, R.87, T.93, R.104, V.111, G.112, N.114 Chain C: E.151 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:K.11, B:N.114, B:N.114 Water bridges: B:K.11, B:R.87, B:R.87, B:R.87, B:R.104, B:R.104, B:R.104, B:G.112 Salt bridges: B:R.87, B:R.104, C:E.151 pi-Stacking: B:F.59, B:F.59 GDP.5: 13 residues within 4Å: Chain A: E.151 Chain C: K.11, Y.51, L.54, F.59, L.63, R.87, T.93, R.104, V.111, G.112, N.114 Ligands: MG.4 16 PLIP interactions: 15 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:K.11, C:N.114, C:N.114 Water bridges: C:K.11, C:Y.51, C:R.87, C:R.87, C:R.104, C:R.104, C:R.104, C:G.112 Salt bridges: C:R.87, C:R.104, A:E.151 pi-Stacking: C:F.59, C:F.59 GDP.6: 11 residues within 4Å: Chain D: K.11, Y.51, L.54, F.59, L.63, R.87, T.93, R.104, V.111, N.114 Chain F: E.151 13 PLIP interactions: 12 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:K.11, D:N.114, D:N.114 Water bridges: D:K.11, D:R.104, D:R.104, D:R.104, D:G.118 Salt bridges: D:R.87, D:R.104, F:E.151 pi-Stacking: D:F.59, D:F.59 GDP.7: 12 residues within 4Å: Chain D: E.151 Chain E: K.11, Y.51, L.54, F.59, L.63, R.87, T.93, R.104, V.111, G.112, N.114 11 PLIP interactions: 10 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:K.11, E:N.114, E:N.114 Water bridges: E:K.11, E:R.87, E:G.112 Salt bridges: E:R.87, E:R.104, D:E.151 pi-Stacking: E:F.59, E:F.59 GDP.8: 12 residues within 4Å: Chain E: E.151 Chain F: K.11, Y.51, L.54, F.59, L.63, R.87, T.93, R.104, V.111, G.112, N.114 13 PLIP interactions: 12 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:K.11, F:N.114, F:N.114 Water bridges: F:K.11, F:R.87, F:R.104, F:R.104, F:H.117 Salt bridges: F:R.87, F:R.104, E:E.151 pi-Stacking: F:F.59, F:F.59

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morera, S. et al., X-ray structure of human nucleoside diphosphate kinase B complexed with GDP at 2 A resolution. Structure (1995)

Release Date

1996-04-03

Peptides

NUCLEOSIDE DIPHOSPHATE KINASE: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

NUCLEOSIDE DIPHOSPHATE KINASE

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