SMTL ID : 5j2m.1

HIV-1 reverse transcriptase in complex with DNA and EFdA-triphosphate, a translocation-defective RT inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.43 Å

Oligo State

hetero-1-1-mer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.110, V.111, D.185 Ligands: 6FN.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.110, A:D.110, A:V.111, A:D.185 MG.2: 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.2 MG.3: 5 residues within 4Å: Chain A: D.110, D.185, D.186 Chain C: G.21 Ligands: 6FN.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.110, A:D.185, H2O.5

1 x 6FN: 2'-deoxy-4'-ethynyl-2-fluoroadenosine 5'-(tetrahydrogen triphosphate)(Non-covalent)

6FN.4: 21 residues within 4Å: Chain A: K.65, K.70, R.72, L.74, D.110, V.111, G.112, D.113, A.114, Y.115, Q.151, G.152, F.160, M.184, D.185, K.220 Chain C: G.21 Chain D: T.5, C.6 Ligands: MG.1, MG.3 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:A.114, A:Y.115, A:Y.115, A:F.160, A:D.185 Hydrogen bonds: A:R.72, A:V.111, A:D.113, A:D.113, A:A.114, A:Y.115, A:D.185 Water bridges: A:K.65, A:K.65, A:K.70, A:K.70, A:F.116, A:Q.151, A:K.220 Salt bridges: A:K.65, A:K.65, A:K.70, A:R.72, A:R.72, A:K.220, A:K.220, A:K.220

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

HIV-1 reverse transcriptase p51 subunit: A
HIV-1 reverse transcriptase p51 subunit: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

HIV-1 reverse transcriptase p51 subunit

HIV-1 reverse transcriptase p51 subunit

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