SMTL ID : 1lwx.1

AZT DIPHOSPHATE BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-hexamer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: E.58, R.92 Ligands: AZD.2 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain C: H.122 Ligands: AZD.5 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain D: E.58, R.92 Ligands: AZD.7 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain F: H.122 Ligands: AZD.10 No protein-ligand interaction detected (PLIP)

6 x AZD: 3'-AZIDO-3'-DEOXYTHYMIDINE-5'-DIPHOSPHATE(Non-covalent)

AZD.2: 14 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, A.119, I.121, H.122 Ligands: MG.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.64 Hydrogen bonds: A:Y.56, A:T.98, A:R.109, A:I.121 Water bridges: A:R.92, A:G.123 Salt bridges: A:H.59, A:R.92, A:R.109 pi-Stacking: A:F.64 AZD.3: 13 residues within 4Å: Chain B: K.16, Y.56, H.59, R.62, F.64, L.68, R.92, T.98, R.109, V.116, A.119, I.121, H.122 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:F.64, B:T.98 Hydrogen bonds: B:K.16, B:Y.56, B:T.98, B:T.98, B:T.98, B:R.109, B:I.121 Water bridges: B:R.92, B:R.92, B:R.92, B:R.92, B:R.92, B:G.123 Salt bridges: B:H.59, B:R.92, B:R.109 pi-Stacking: B:F.64 AZD.5: 15 residues within 4Å: Chain C: K.16, Y.56, H.59, R.62, F.64, L.68, R.92, T.98, R.109, V.116, G.117, A.119, I.121, H.122 Ligands: MG.4 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:F.64, C:V.116, C:A.119 Hydrogen bonds: C:Y.56, C:T.98, C:R.109, C:I.121 Water bridges: C:R.92, C:R.92, C:R.109, C:G.123 Salt bridges: C:H.59, C:R.92, C:R.109 pi-Stacking: C:F.64 AZD.7: 14 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, A.119, I.121, H.122 Ligands: MG.6 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:F.64 Hydrogen bonds: D:T.98, D:R.109 Water bridges: D:R.92, D:G.123, D:D.125 Salt bridges: D:H.59, D:R.92, D:R.109 pi-Stacking: D:F.64 AZD.8: 13 residues within 4Å: Chain E: K.16, Y.56, H.59, R.62, F.64, L.68, R.92, T.98, R.109, V.116, A.119, I.121, H.122 18 PLIP interactions: 18 interactions with chain E Hydrophobic interactions: E:F.64, E:T.98 Hydrogen bonds: E:K.16, E:Y.56, E:T.98, E:T.98, E:R.109, E:H.122 Water bridges: E:R.92, E:R.92, E:R.92, E:R.92, E:R.92, E:G.123 Salt bridges: E:H.59, E:R.92, E:R.109 pi-Stacking: E:F.64 AZD.10: 15 residues within 4Å: Chain F: K.16, Y.56, H.59, R.62, F.64, L.68, R.92, T.98, R.109, V.116, G.117, A.119, I.121, H.122 Ligands: MG.9 13 PLIP interactions: 13 interactions with chain F Hydrophobic interactions: F:F.64, F:V.116, F:A.119 Hydrogen bonds: F:T.98, F:R.109 Water bridges: F:R.92, F:R.92, F:R.109, F:G.123 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

Xu, Y. et al., X-ray analysis of azido-thymidine diphosphate binding to nucleoside diphosphate kinase. Proc.Natl.Acad.Sci.USA (1997)

Release Date

1997-08-20

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