SMTL ID : 1mn7.1

NDP kinase mutant (H122G;N119S;F64W) in complex with aBAZTTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-hexamer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 3 residues within 4Å: Chain A: R.92, D.125 Ligands: ABT.2 No protein-ligand interaction detected (PLIP) MG.3: 1 residues within 4Å: Ligands: ABT.4 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain C: R.92, D.125 Ligands: ABT.6 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Ligands: ABT.8 No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain E: R.92, D.125 Ligands: ABT.10 No protein-ligand interaction detected (PLIP) MG.11: 1 residues within 4Å: Ligands: ABT.12 No protein-ligand interaction detected (PLIP)

6 x ABT: 3'-AZIDO-3'-DEOXY-THYMIDINE-5'-ALPHA BORANO TRIPHOSPHATE(Non-covalent)

ABT.2: 13 residues within 4Å: Chain A: K.16, Y.56, H.59, W.64, L.68, R.92, T.98, R.109, V.116, S.119, G.122, G.123 Ligands: MG.1 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:W.64, A:L.68 Hydrogen bonds: A:K.16, A:Y.56, A:R.109, A:S.119, A:G.123 Water bridges: A:E.58, A:R.92, A:R.92 Salt bridges: A:K.16, A:R.92, A:R.92, A:R.109, A:R.109 pi-Stacking: A:W.64, A:W.64 ABT.4: 13 residues within 4Å: Chain B: K.16, Y.56, H.59, W.64, L.68, R.92, T.98, R.109, V.116, S.119, G.122, G.123 Ligands: MG.3 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:W.64, B:L.68 Hydrogen bonds: B:K.16, B:Y.56, B:Y.56, B:S.119, B:S.119, B:G.123, B:G.123 Water bridges: B:R.92, B:R.92, B:D.125, B:D.125, B:D.125 Salt bridges: B:K.16, B:R.92, B:R.92, B:R.109, B:R.109 pi-Stacking: B:W.64, B:W.64 ABT.6: 13 residues within 4Å: Chain C: K.16, Y.56, H.59, W.64, L.68, R.92, T.98, R.109, V.116, S.119, G.122, G.123 Ligands: MG.5 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:W.64, C:L.68 Hydrogen bonds: C:K.16, C:Y.56, C:T.98, C:S.119, C:G.123 Water bridges: C:E.58, C:R.92, C:R.92 Salt bridges: C:K.16, C:R.92, C:R.92, C:R.109, C:R.109 pi-Stacking: C:W.64, C:W.64 ABT.8: 13 residues within 4Å: Chain D: K.16, Y.56, H.59, W.64, L.68, R.92, T.98, R.109, V.116, S.119, G.122, G.123 Ligands: MG.7 21 PLIP interactions: 21 interactions with chain D Hydrophobic interactions: D:W.64, D:L.68 Hydrogen bonds: D:K.16, D:Y.56, D:Y.56, D:T.98, D:S.119, D:G.123, D:G.123 Water bridges: D:R.92, D:R.92, D:D.125, D:D.125, D:D.125 Salt bridges: D:K.16, D:R.92, D:R.92, D:R.109, D:R.109 pi-Stacking: D:W.64, D:W.64 ABT.10: 13 residues within 4Å: Chain E: K.16, Y.56, H.59, W.64, L.68, R.92, T.98, R.109, V.116, S.119, G.122, G.123 Ligands: MG.9 17 PLIP interactions: 17 interactions with chain E Hydrophobic interactions: E:W.64, E:L.68 Hydrogen bonds: E:K.16, E:Y.56, E:R.109, E:S.119, E:G.123 Water bridges: E:E.58, E:R.92, E:R.92 Salt bridges: E:K.16, E:R.92, E:R.92, E:R.109, E:R.109 pi-Stacking: E:W.64, E:W.64 ABT.12: 13 residues within 4Å: Chain F: K.16, Y.56, H.59, W.64, L.68, R.92, T.98, R.109, V.116, S.119, G.122, G.123 Ligands: MG.11 20 PLIP interactions: 20 interactions with chain F Hydrophobic interactions: F:W.64, F:L.68 Hydrogen bonds: F:K.16, F:Y.56, F:Y.56, F:S.119, F:G.123, F:G.123 Water bridges: F:R.92, F:R.92, F:D.125, F:D.125, F:D.125 Salt bridges: F:K.16, F:R.92, F:R.92, F:R.109, F:R.109 pi-Stacking: F:W.64, F:W.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

gallois-montbrun, s. et al., Improving nucleoside diphosphate kinase for antiviral nucleotide analogs activation. J.BIOL.CHEM. (2002)

Release Date

2002-10-02

Peptides

NDP kinase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

NDP kinase