SMTL ID : 1ndp.1

ADENOSINE 5'-DIPHOSPHATE BINDING AND THE ACTIVE SITE OF NUCLEOSIDE DIPHOSPHATE KINASE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

6 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 10 residues within 4Å: Chain A: K.16, H.59, F.64, L.68, R.92, T.98, R.109, V.116, G.117, N.119 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:K.16, A:R.109, 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 ADP.3: 12 residues within 4Å: Chain B: K.16, Y.56, H.59, F.64, L.68, R.92, T.98, R.109, V.116, G.117, N.119 Ligands: MG.2 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:K.16, B:T.98, B:R.109, B:N.119, B:N.119 Water bridges: B:K.16, B:Y.56, B:R.92, B:R.92, B:R.92, B:H.122, B:H.122, B:H.122, B:H.122 Salt bridges: B:H.59, B:R.92, B:R.109 pi-Stacking: B:F.64, B:F.64 ADP.4: 10 residues within 4Å: Chain C: K.16, H.59, F.64, L.68, R.92, T.98, R.109, V.116, G.117, N.119 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:K.16, C:R.109, C:N.119, C:N.119 Salt bridges: C:H.59, C:R.92, C:R.109 pi-Stacking: C:F.64, C:F.64 ADP.6: 12 residues within 4Å: Chain D: K.16, Y.56, H.59, F.64, L.68, R.92, T.98, R.109, V.116, G.117, N.119 Ligands: MG.5 19 PLIP interactions: 19 interactions with chain D Hydrogen bonds: D:K.16, D:T.98, D:R.109, D:N.119, D:N.119 Water bridges: D:K.16, D:Y.56, D:R.92, D:R.92, D:R.92, D:H.122, D:H.122, D:H.122, D:H.122 Salt bridges: D:H.59, D:R.92, D:R.109 pi-Stacking: D:F.64, D:F.64 ADP.7: 10 residues within 4Å: Chain E: K.16, H.59, F.64, L.68, R.92, T.98, R.109, V.116, G.117, N.119 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:K.16, E:R.109, E:N.119, E:N.119 Salt bridges: E:H.59, E:R.92, E:R.109 pi-Stacking: E:F.64, E:F.64 ADP.9: 12 residues within 4Å: Chain F: K.16, Y.56, H.59, F.64, L.68, R.92, T.98, R.109, V.116, G.117, N.119 Ligands: MG.8 19 PLIP interactions: 19 interactions with chain F Hydrogen bonds: F:K.16, F:T.98, F:R.109, F:N.119, F:N.119 Water bridges: F:K.16, F:Y.56, F:R.92, F:R.92, F:R.92, F:H.122, F:H.122, F:H.122, F:H.122 Salt bridges: F:H.59, F:R.92, F:R.109 pi-Stacking: F:F.64, F:F.64

3 x MG: MAGNESIUM ION(Non-functional Binders)

MG.2: 1 residues within 4Å: Ligands: ADP.3 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Ligands: ADP.6 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Ligands: ADP.9 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morera, S. et al., Adenosine 5'-diphosphate binding and the active site of nucleoside diphosphate kinase. Biochemistry (1994)

Release Date

1994-04-30

Peptides

NUCLEOSIDE DIPHOSPHATE KINASE: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

NUCLEOSIDE DIPHOSPHATE KINASE

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