SMTL ID : 5j2p.1

HIV-1 reverse transcriptase in complex with DNA that has incorporated EFdA-MP at the P-(post-translocation) site and a second EFdA-MP at the N-(pre-translocation) site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.53 Å

Oligo State

hetero-1-1-mer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.443, G.444, E.478, D.498 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.443, A:E.478, A:D.498, H2O.2, H2O.6

2 x 6FM: 2'-deoxy-4'-ethynyl-2-fluoroadenosine 5'-(dihydrogen phosphate)(Non-covalent)

6FM.2: 11 residues within 4Å: Chain A: R.72, A.114, Y.115, Q.151, G.152, F.160, M.184, D.185 Chain D: T.5, T.6 Ligands: 6FM.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:A.114, A:Y.115, A:Y.115, A:F.160, A:D.185 Hydrogen bonds: A:A.114, A:Y.115 Water bridges: A:R.72, A:F.116, A:K.220 Salt bridges: A:R.72 6FM.3: 10 residues within 4Å: Chain A: Y.183, M.184, D.185, D.186, M.230, G.231 Chain C: C.20 Chain D: T.6, G.7 Ligands: 6FM.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.183, A:M.184, A:D.186 Hydrogen bonds: A:M.230, A:G.231 Water bridges: A:K.66, A:Q.242

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Salie, Z.L. et al., Structural basis of HIV inhibition by translocation-defective RT inhibitor 4'-ethynyl-2-fluoro-2'-deoxyadenosine (EFdA). Proc.Natl.Acad.Sci.USA (2016)

Release Date

2016-08-03

Peptides

reverse transcriptase, p66 domain: A
reverse transcriptase, p51 domain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

reverse transcriptase, p66 domain

reverse transcriptase, p51 domain

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