SMTL ID : 6wpj.1

Structure of HIV-1 Reverse Transcriptase (RT) in complex with dsDNA and d4T

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.73 Å

Oligo State

hetero-1-1-mer

Ligands

1 x D4T: 2',3'-DEHYDRO-2',3'-DEOXY-THYMIDINE 5'-TRIPHOSPHATE(Non-covalent)

D4T.1: 16 residues within 4Å: Chain A: K.66, R.73, D.111, V.112, G.113, D.114, A.115, Y.116, Q.152, M.185, D.186, K.221 Chain C: G.21 Chain D: A.5, C.6 Ligands: MG.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.116, A:Y.116, A:Q.152 Hydrogen bonds: A:D.114, A:A.115 Water bridges: A:Y.116 Salt bridges: A:K.66, A:K.66, A:R.73, A:R.73, A:K.221, A:K.221, A:K.221 pi-Cation interactions: A:R.73

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.111, V.112, D.186, K.221 Ligands: D4T.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.111, A:V.112, A:D.186 MG.3: 4 residues within 4Å: Chain A: D.444, G.445, E.479, D.499 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.444, A:E.479, A:D.499, A:D.499

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 4 residues within 4Å: Chain A: G.437, N.461, R.462 Chain B: A.300 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.437, A:N.461, A:N.461 Salt bridges: A:R.462

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bertoletti, N. et al., Post-Catalytic Complexes with Emtricitabine or Stavudine and HIV-1 Reverse Transcriptase Reveal New Mechanistic Insights for Nucleotide Incorporation and Drug Resistance. Molecules (2020)

Release Date

2020-11-04

Peptides

Reverse transcriptase/ribonuclease H: A
p51 RT: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Reverse transcriptase/ribonuclease H

p51 RT

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