SMTL ID : 1mn9.1

NDP kinase mutant (H122G) complex with RTP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-hexamer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: E.58, D.125 Ligands: RTP.2 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain B: E.58 Ligands: RTP.3 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain C: E.58, D.125 Ligands: RTP.4 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain D: E.58, D.125 Ligands: RTP.8 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain E: E.58 Ligands: RTP.9 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain F: E.58, D.125 Ligands: RTP.10 No protein-ligand interaction detected (PLIP)

6 x RTP: RIBAVIRIN TRIPHOSPHATE(Non-covalent)

RTP.2: 13 residues within 4Å: Chain A: K.16, Y.56, H.59, F.64, L.68, R.92, T.98, R.109, V.116, N.119, G.122, G.123 Ligands: MG.1 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:K.16, A:Y.56, A:T.98, A:G.117, A:N.119, A:G.123 Water bridges: A:R.92, A:D.125, A:D.125 Salt bridges: A:K.16, A:H.59, A:R.92, A:R.92, A:R.109 pi-Stacking: A:F.64 RTP.3: 13 residues within 4Å: Chain B: K.16, Y.56, H.59, F.64, L.68, R.92, T.98, R.109, V.116, N.119, G.122, G.123 Ligands: MG.5 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:K.16, B:Y.56, B:R.92, B:R.109, B:G.117, B:N.119, B:G.123, B:G.123 Water bridges: B:R.92, B:R.92 Salt bridges: B:K.16, B:H.59, B:R.92, B:R.109 pi-Stacking: B:F.64 RTP.4: 13 residues within 4Å: Chain C: K.16, Y.56, H.59, F.64, L.68, R.92, T.98, R.109, V.116, N.119, G.122, G.123 Ligands: MG.6 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:K.16, C:Y.56, C:T.98, C:G.117, C:N.119, C:G.123 Salt bridges: C:K.16, C:H.59, C:R.92, C:R.92, C:R.109 pi-Stacking: C:F.64 RTP.8: 13 residues within 4Å: Chain D: K.16, Y.56, H.59, F.64, L.68, R.92, T.98, R.109, V.116, N.119, G.122, G.123 Ligands: MG.7 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:K.16, D:G.117, D:N.119, D:G.123 Water bridges: D:R.92, D:R.92, D:R.92 Salt bridges: D:K.16, D:H.59, D:R.92, D:R.92, D:R.109 pi-Stacking: D:F.64 RTP.9: 13 residues within 4Å: Chain E: K.16, Y.56, H.59, F.64, L.68, R.92, T.98, R.109, V.116, N.119, G.122, G.123 Ligands: MG.11 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:K.16, E:R.92, E:R.109, E:G.117, E:N.119, E:G.123, E:G.123 Water bridges: E:R.92, E:R.92 Salt bridges: E:K.16, E:H.59, E:R.92, E:R.109 pi-Stacking: E:F.64 RTP.10: 13 residues within 4Å: Chain F: K.16, Y.56, H.59, F.64, L.68, R.92, T.98, R.109, V.116, N.119, G.122, G.123 Ligands: MG.12 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:K.16, F:G.117, F:N.119, F:G.123 Salt bridges: F:K.16, F:H.59, F:R.92, F:R.92, F:R.109 pi-Stacking: F:F.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gallois-montbrun, S. et al., Structural Analysis of the Activation of Ribavirin Analogs by NDP Kinase: Comparison with Other Ribavirin Targets. MOL.PHARMACOL. (2003)

Release Date

2003-03-18

Peptides

NDP kinase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

NDP kinase

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