SMTL ID : 1ndc.1

X-RAY STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE COMPLEXED WITH DTDP AND MG2+ AT 2 A RESOLUTION

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-hexamer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: D.125 Ligands: TYD.2 No protein-ligand interaction detected (PLIP) MG.3: 2 residues within 4Å: Chain B: D.125 Ligands: TYD.4 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain C: D.125 Ligands: TYD.6 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain D: D.125 Ligands: TYD.8 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain E: D.125 Ligands: TYD.10 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain F: D.125 Ligands: TYD.12 No protein-ligand interaction detected (PLIP)

6 x TYD: THYMIDINE-5'-DIPHOSPHATE(Non-covalent)

TYD.2: 10 residues within 4Å: Chain A: K.16, H.59, F.64, L.68, R.92, T.98, R.109, V.116, N.119 Ligands: MG.1 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:F.64 Hydrogen bonds: A:K.16, A:T.98, A:T.98, A:R.109, A:N.119 Water bridges: A:Y.56, A:Y.56, A:R.92, A:R.92, A:R.92, A:R.92, A:H.122 Salt bridges: A:H.59, A:R.92, A:R.109 pi-Stacking: A:F.64 TYD.4: 10 residues within 4Å: Chain B: K.16, H.59, F.64, L.68, R.92, T.98, R.109, V.116, N.119 Ligands: MG.3 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:F.64 Hydrogen bonds: B:K.16, B:T.98, B:T.98, B:R.109, B:N.119 Water bridges: B:Y.56, B:Y.56, B:R.92, B:R.92, B:R.92, B:R.92, B:H.122 Salt bridges: B:H.59, B:R.92, B:R.109 pi-Stacking: B:F.64 TYD.6: 10 residues within 4Å: Chain C: K.16, H.59, F.64, L.68, R.92, T.98, R.109, V.116, N.119 Ligands: MG.5 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:F.64 Hydrogen bonds: C:K.16, C:T.98, C:T.98, C:R.109, C:N.119 Water bridges: C:Y.56, C:Y.56, C:R.92, C:R.92, C:R.92, C:R.92, C:H.122 Salt bridges: C:H.59, C:R.92, C:R.109 pi-Stacking: C:F.64 TYD.8: 10 residues within 4Å: Chain D: K.16, H.59, F.64, L.68, R.92, T.98, R.109, V.116, N.119 Ligands: MG.7 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:F.64 Hydrogen bonds: D:K.16, D:T.98, D:R.109, D:N.119 Water bridges: D:Y.56, D:R.92, D:R.92, D:R.92, D:R.92, D:H.122, D:H.122 Salt bridges: D:H.59, D:R.92, D:R.109 pi-Stacking: D:F.64 TYD.10: 10 residues within 4Å: Chain E: K.16, H.59, F.64, L.68, R.92, T.98, R.109, V.116, N.119 Ligands: MG.9 16 PLIP interactions: 16 interactions with chain E Hydrophobic interactions: E:F.64 Hydrogen bonds: E:K.16, E:T.98, E:R.109, E:N.119 Water bridges: E:Y.56, E:R.92, E:R.92, E:R.92, E:R.92, E:H.122, E:H.122 Salt bridges: E:H.59, E:R.92, E:R.109 pi-Stacking: E:F.64 TYD.12: 10 residues within 4Å: Chain F: K.16, H.59, F.64, L.68, R.92, T.98, R.109, V.116, N.119 Ligands: MG.11 16 PLIP interactions: 16 interactions with chain F Hydrophobic interactions: F:F.64 Hydrogen bonds: F:K.16, F:T.98, F:R.109, F:N.119 Water bridges: F:Y.56, F:R.92, F:R.92, F:R.92, F:R.92, F:H.122, F:H.122 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

Cherfils, J. et al., X-ray structure of nucleoside diphosphate kinase complexed with thymidine diphosphate and Mg2+ at 2-A resolution. Biochemistry (1994)

Release Date

1994-06-22

Peptides

NUCLEOSIDE DIPHOSPHATE KINASE: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

NUCLEOSIDE DIPHOSPHATE KINASE

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