SMTL ID : 3fkb.1

Structure of NDPK H122G and tenofovir-diphosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-hexamer

Ligands

5 x TNM: [(2R)-1-(6-aminopurin-9-yl)propan-2-yl]oxymethyl-phosphonooxy-phosphinic acid(Non-covalent)

TNM.1: 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.2 18 PLIP interactions: 15 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.64 Hydrogen bonds: A:K.16, A:N.119 Water bridges: A:R.92, A:R.92, A:R.92, A:R.92, A:R.92, A:T.98, A:R.109, A:G.123, B:E.155, B:E.155, B:E.155 Salt bridges: A:R.92, A:R.109 pi-Stacking: A:F.64, A:F.64 TNM.4: 11 residues within 4Å: Chain B: K.16, H.59, F.64, L.68, R.92, T.98, R.109, V.116, G.117, N.119 Ligands: MG.5 18 PLIP interactions: 17 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:F.64 Hydrogen bonds: B:T.98, B:N.119 Water bridges: B:K.16, B:Y.56, B:R.92, B:R.92, B:R.92, B:R.92, B:R.92, B:R.92, B:R.109, B:R.109, B:G.123, C:E.155 Salt bridges: B:R.92, B:R.109 pi-Stacking: B:F.64 TNM.7: 13 residues within 4Å: Chain A: E.155 Chain C: K.16, Y.56, H.59, F.64, L.68, R.92, R.109, V.116, G.117, N.119 Ligands: MG.8, GOL.9 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:F.64 Hydrogen bonds: C:K.16, C:Y.56, C:N.119 Water bridges: C:R.92, C:R.92, C:R.92, C:R.92, C:R.92, C:G.123, C:G.123 Salt bridges: C:R.92, C:R.109 pi-Stacking: C:F.64, C:F.64 TNM.14: 11 residues within 4Å: Chain D: E.155 Chain E: K.16, H.59, F.64, L.68, R.92, T.98, R.109, V.116, N.119 Ligands: MG.15 19 PLIP interactions: 18 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:F.64 Hydrogen bonds: E:K.16, E:N.119, D:E.155 Water bridges: E:R.92, E:R.92, E:R.92, E:R.92, E:T.98, E:T.98, E:T.98, E:T.98, E:R.109, E:G.123, E:G.123 Salt bridges: E:R.92, E:R.109 pi-Stacking: E:F.64, E:F.64 TNM.16: 12 residues within 4Å: Chain E: E.155 Chain F: K.16, H.59, F.64, L.68, R.92, T.98, R.109, V.116, G.117, N.119 Ligands: MG.17 17 PLIP interactions: 16 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:F.64 Hydrogen bonds: F:K.16, F:N.119, E:E.155 Water bridges: F:Y.56, F:Y.56, F:R.92, F:R.92, F:R.92, F:R.92, F:R.92, F:T.98, F:T.98, F:G.123 Salt bridges: F:R.92, F:R.109 pi-Stacking: F:F.64

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

MG.2: 1 residues within 4Å: Ligands: TNM.1 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Ligands: TNM.4 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Ligands: TNM.7 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain D: E.58 Ligands: TNV.10 No protein-ligand interaction detected (PLIP) MG.15: 1 residues within 4Å: Ligands: TNM.14 No protein-ligand interaction detected (PLIP) MG.17: 1 residues within 4Å: Ligands: TNM.16 No protein-ligand interaction detected (PLIP)

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 5 residues within 4Å: Chain A: E.146, K.148 Chain D: S.74, G.75, P.76 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:K.148, D:S.74 EDO.6: 4 residues within 4Å: Chain B: V.38, K.148 Chain E: V.20, A.21 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:K.148, E:A.21 Water bridges: B:K.148, B:N.150 EDO.13: 7 residues within 4Å: Chain D: V.38, V.147, K.148, P.149, N.150, L.153, Y.154 5 PLIP interactions: 5 interactions with chain D Water bridges: D:N.7, D:V.38, D:V.147, D:K.148, D:N.150 EDO.18: 4 residues within 4Å: Chain F: G.67, S.70, F.71, S.74 2 PLIP interactions: 2 interactions with chain F Water bridges: F:R.118, F:R.118 EDO.19: 2 residues within 4Å: Chain F: V.6, N.7 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.7

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 5 residues within 4Å: Chain C: R.92, G.96, V.97, T.98 Ligands: TNM.7 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.92, C:T.98, C:T.98 Water bridges: C:R.109 GOL.12: 2 residues within 4Å: Chain D: N.99, L.101 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:N.99 Water bridges: F:G.86

1 x TNV: [2-(6-AMINO-9H-PURIN-9-YL)-1-METHYLETHOXY]METHYL-TRIPHOSPHATE(Non-covalent)

TNV.10: 14 residues within 4Å: Chain D: K.16, Y.56, E.58, H.59, F.64, R.92, T.98, R.109, V.116, G.117, N.119, G.123 Chain F: E.155 Ligands: MG.11 23 PLIP interactions: 22 interactions with chain D, 1 interactions with chain F Hydrophobic interactions: D:F.64 Hydrogen bonds: D:K.16, D:N.119, D:G.123, F:E.155 Water bridges: D:Y.56, D:R.92, D:R.92, D:R.92, D:R.92, D:R.92, D:T.98, D:R.109, D:R.109, D:R.109, D:G.122, D:G.123 Salt bridges: D:H.59, D:R.92, D:R.92, D:R.109 pi-Stacking: D:F.64, D:F.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koch, K. et al., Nucleoside diphosphate kinase and the activation of antiviral phosphonate analogs of nucleotides: binding mode and phosphorylation of tenofovir derivatives. Nucleosides Nucleotides Nucleic Acids (2009)

Release Date

2009-09-29

Peptides

Nucleoside diphosphate kinase, cytosolic: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Nucleoside diphosphate kinase, cytosolic

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