SMTL ID : 1b99.1

3'-FLUORO-URIDINE DIPHOSPHATE BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-hexamer

Ligands

1 x FUP: 2',3'-DIDEOXY-3'-FLUORO-URIDIDINE-5'-DIPHOSPHATE(Non-covalent)

FUP.1: 11 residues within 4Å: Chain A: K.16, Y.56, H.59, F.64, L.68, R.92, T.98, R.109, V.116, G.117, N.119 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.116 Hydrogen bonds: A:T.98, A:T.98, A:N.119 Water bridges: A:R.109, A:R.109 Salt bridges: A:H.59, A:R.92, A:R.109 pi-Stacking: A:F.64 Halogen bonds: A:K.16, A:Y.56

5 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.2: 4 residues within 4Å: Chain B: H.59, R.92, T.98, R.109 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.109, B:R.109 Water bridges: B:N.119, B:N.119, B:H.122 Salt bridges: B:H.59, B:R.92 POP.3: 5 residues within 4Å: Chain C: H.59, R.92, T.98, R.109, N.119 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:T.98, C:N.119 Salt bridges: C:H.59, C:R.92, C:R.109 POP.4: 4 residues within 4Å: Chain D: H.59, R.92, T.98, R.109 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.98, D:N.119 Salt bridges: D:H.59, D:R.92, D:R.109 POP.5: 3 residues within 4Å: Chain E: R.92, T.98, R.109 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:T.98, E:T.98 Water bridges: E:N.119, E:N.119 Salt bridges: E:H.59, E:R.92, E:R.109 POP.6: 5 residues within 4Å: Chain F: H.59, R.92, T.98, R.109, D.125 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:T.98, F:N.119, F:D.125, F:D.125 Salt bridges: F:H.59, F:R.92, F:R.109

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gonin, P. et al., Catalytic mechanism of nucleoside diphosphate kinase investigated using nucleotide analogues, viscosity effects, and X-ray crystallography. Biochemistry (1999)

Release Date

1999-06-28

Peptides

PROTEIN (NUCLEOSIDE DIPHOSPHATE KINASE): ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

PROTEIN (NUCLEOSIDE DIPHOSPHATE KINASE)

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