SMTL ID : 4cp5.1

ndpK in complex with (Rp)-SPMPApp

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

homo-hexamer

Ligands

6 x EOI: [[(2R)-1-(6-aminopurin-9-yl)propan-2-yl]oxymethyl-sulfanyl-phosphoryl] phosphono hydrogen phosphate(Non-covalent)

EOI.1: 11 residues within 4Å: Chain A: K.16, E.58, H.59, F.64, L.68, R.92, T.98, R.109, V.116, N.119, G.123 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:F.64 Hydrogen bonds: A:K.16, A:E.58, A:N.119 Water bridges: A:E.58, A:H.59, A:R.109, A:R.109, A:R.109, A:R.109, A:G.123 Salt bridges: A:H.59, A:R.92, A:R.92, A:R.109 pi-Stacking: A:F.64, A:F.64 EOI.2: 11 residues within 4Å: Chain B: K.16, Y.56, H.59, F.64, R.92, T.98, R.109, V.116, N.119, G.122, D.125 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:K.16, B:R.109, B:N.119 Water bridges: B:R.92, B:R.109, B:R.109, B:G.123 Salt bridges: B:R.92, B:R.92, B:R.109 pi-Stacking: B:F.64, B:F.64 EOI.3: 11 residues within 4Å: Chain C: K.16, H.59, F.64, L.68, R.92, T.98, R.109, V.116, N.119, G.122, D.125 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:F.64 Hydrogen bonds: C:K.16, C:N.119, C:D.125 Water bridges: C:E.58, C:R.92, C:G.123, C:G.123 Salt bridges: C:R.92, C:R.92, C:R.109 pi-Stacking: C:F.64, C:F.64 EOI.4: 11 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, D.125 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:F.64 Hydrogen bonds: D:K.16, D:N.119, D:G.123, D:D.125 Water bridges: D:E.58, D:E.58, D:R.92, D:R.92 Salt bridges: D:R.92, D:R.92, D:R.109 pi-Stacking: D:F.64, D:F.64 EOI.5: 11 residues within 4Å: Chain E: K.16, H.59, F.64, L.68, R.92, T.98, R.109, V.116, N.119, G.122, D.125 15 PLIP interactions: 15 interactions with chain E Hydrophobic interactions: E:F.64 Hydrogen bonds: E:N.119, E:G.123 Water bridges: E:E.58, E:H.59, E:R.92, E:R.92, E:R.92, E:R.109, E:R.109 Salt bridges: E:R.92, E:R.92, E:R.109 pi-Stacking: E:F.64, E:F.64 EOI.6: 12 residues within 4Å: Chain F: K.16, H.59, F.64, L.68, R.92, T.98, R.109, V.116, N.119, G.122, G.123, D.125 14 PLIP interactions: 14 interactions with chain F Hydrophobic interactions: F:F.64 Hydrogen bonds: F:K.16, F:H.59, F:T.98, F:N.119 Water bridges: F:R.92, F:R.92, F:R.92, F:D.125 Salt bridges: F:R.92, F:R.92, F:R.109 pi-Stacking: F:F.64, F:F.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Priet, S. et al., Enzymatic Synthesis of Acyclic Nucleoside Thiophosphonate Diphosphates: Effect of the Alpha-Phosphorus Configuration on HIV-1 RT Activity. Antiviral Res. (2015)

Release Date

2015-02-11

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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