SMTL ID : 1bux.1

3'-PHOSPHORYLATED NUCLEOTIDES BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-hexamer

Ligands

6 x PPS: 3'-PHOSPHATE-ADENOSINE-5'-PHOSPHATE SULFATE(Non-covalent)

PPS.1: 10 residues within 4Å: Chain A: K.16, Y.56, H.59, R.62, F.64, L.68, T.98, R.109, N.119, H.122 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Y.56, A:Y.56, A:T.98, A:R.109, A:N.119 Salt bridges: A:K.16, A:H.59, A:R.62, A:H.122 pi-Stacking: A:F.64 PPS.2: 11 residues within 4Å: Chain B: K.16, Y.56, H.59, F.64, L.68, T.98, R.109, V.116, N.119, I.121, H.122 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Y.56, B:T.98, B:N.119 Salt bridges: B:K.16, B:H.59, B:R.109, B:H.122 pi-Stacking: B:F.64 PPS.3: 11 residues within 4Å: Chain C: K.16, Y.56, H.59, F.64, L.68, R.92, T.98, V.116, N.119, I.121, H.122 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:Y.56, C:Y.56, C:R.92, C:T.98, C:N.119, C:I.121 Salt bridges: C:K.16, C:H.59, C:H.122 pi-Stacking: C:F.64, C:F.64 PPS.4: 10 residues within 4Å: Chain D: K.16, Y.56, H.59, R.62, F.64, L.68, T.98, R.109, N.119, H.122 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:Y.56, D:R.109, D:N.119 Salt bridges: D:K.16, D:H.59, D:R.62, D:H.122 pi-Stacking: D:F.64 PPS.5: 11 residues within 4Å: Chain E: K.16, Y.56, H.59, F.64, L.68, T.98, R.109, V.116, N.119, I.121, H.122 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:N.119 Salt bridges: E:K.16, E:H.59, E:R.109, E:H.122 pi-Stacking: E:F.64 PPS.6: 11 residues within 4Å: Chain F: K.16, Y.56, H.59, F.64, L.68, R.92, T.98, V.116, N.119, I.121, H.122 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:Y.56, F:R.92, F:N.119, F:I.121 Salt bridges: F:K.16, F:H.59, F:H.122 pi-Stacking: F:F.64, F:F.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schneider, B. et al., 3'-Phosphorylated nucleotides are tight binding inhibitors of nucleoside diphosphate kinase activity. J.Biol.Chem. (1998)

Release Date

1999-04-27

Peptides

NUCLEOSIDE DIPHOSPHATE KINASE: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

NUCLEOSIDE DIPHOSPHATE KINASE

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