SMTL ID : 1hiy.1

Binding of nucleotides to NDP kinase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-hexamer

Ligands

6 x 3AN: 3'-DEOXY 3'-AMINO ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cervoni, L. et al., Binding of Nucleotides to Nucleoside Diphosphate Kinase: A Calorimetric Study. Biochemistry (2001)

Release Date

2001-05-31

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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