SMTL ID : 1t05.1

HIV-1 reverse transcriptase crosslinked to template-primer with tenofovir-diphosphate bound as the incoming nucleotide substrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-1-1-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain C: D.110, V.111, D.185, K.219 Ligands: TNV.3 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.110, C:V.111, C:D.185 MG.2: 3 residues within 4Å: Chain C: D.443, E.478, D.498 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.443, C:D.443, C:D.498

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

TNV.3: 15 residues within 4Å: Chain A: T.5, C.6 Chain B: G.21 Chain C: K.65, R.72, D.110, V.111, G.112, D.113, A.114, Y.115, Q.151, D.185, K.219 Ligands: MG.1 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:R.72, C:R.72, C:D.113, C:D.113, C:D.113, C:A.114, C:K.219 Salt bridges: C:K.65, C:K.65, C:R.72, C:K.219 pi-Cation interactions: C:R.72

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain C: K.101, K.102, K.103, V.106, Y.188, H.235, P.236, Y.318 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.103, C:K.103, C:Y.188, C:Y.188, C:Y.318 GOL.5: 6 residues within 4Å: Chain C: E.328, Q.340, Y.342, P.345, N.348 Ligands: GOL.6 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.340, C:Y.342 Water bridges: C:Y.342 GOL.6: 3 residues within 4Å: Chain C: Q.330, Q.340 Ligands: GOL.5 No protein-ligand interaction detected (PLIP) GOL.7: 6 residues within 4Å: Chain D: D.76, R.78, E.79, K.82, E.413 Ligands: GOL.8 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:D.76, D:R.78, D:R.78, D:E.79, D:K.82, D:E.413 GOL.8: 2 residues within 4Å: Chain D: V.21 Ligands: GOL.7 2 PLIP interactions: 2 interactions with chain D Water bridges: D:W.24, D:E.399

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tuske, S. et al., Structures of HIV-1 RT-DNA complexes before and after incorporation of the anti-AIDS drug tenofovir. Nat.Struct.Mol.Biol. (2004)

Release Date

2004-05-11

Peptides

POL polyprotein: C
POL polyprotein: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

D
B

POL polyprotein

POL polyprotein

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