SMTL ID : 6wpf.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.53 Å

Oligo State

hetero-1-1-mer

Ligands

1 x D4M: [(5R)-5-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-2,5-DIHYDROFURAN-2-YL]METHYL DIHYDROGEN PHOSPHATE(Non-covalent)

D4M.1: 8 residues within 4Å: Chain A: G.21 Chain C: K.67, D.111, K.221, Q.223, L.229 Ligands: MG.3, D4T.7 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:L.229 Hydrogen bonds: C:K.67 Water bridges: C:K.221, C:K.221, C:Q.243 Salt bridges: C:K.67, C:K.221

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

SO4.2: 4 residues within 4Å: Chain A: G.15, G.16 Chain B: G.10, C.11 No protein-ligand interaction detected (PLIP) SO4.4: 2 residues within 4Å: Chain B: G.7, G.8 No protein-ligand interaction detected (PLIP) SO4.8: 6 residues within 4Å: Chain C: G.437, A.438, E.439, N.461, R.462 Chain D: A.300 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.437, C:N.461 Salt bridges: C:R.462 SO4.9: 7 residues within 4Å: Chain C: K.102, K.104, V.107, Y.189, H.236, P.237, Y.319 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.102, C:K.104, C:Y.189

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 7 residues within 4Å: Chain A: G.21 Chain C: D.111, D.186, K.221 Ligands: D4M.1, MG.6, D4T.7 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.111, C:D.111, C:D.186 MG.5: 4 residues within 4Å: Chain C: D.444, G.445, E.479, D.499 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.444, C:E.479, C:D.499, C:D.499, H2O.1 MG.6: 6 residues within 4Å: Chain C: D.111, V.112, D.186, K.221 Ligands: MG.3, D4T.7 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.111, C:V.112, C:D.186

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

D4T.7: 19 residues within 4Å: Chain A: G.21 Chain B: A.5, C.6 Chain C: K.66, K.71, R.73, D.111, V.112, G.113, D.114, A.115, Y.116, Q.152, M.185, D.186, K.221 Ligands: D4M.1, MG.3, MG.6 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:Y.116, C:Y.116 Hydrogen bonds: C:V.112, C:D.114, C:A.115, C:Y.116 Water bridges: C:Q.152 Salt bridges: C:K.66, C:K.66, C:K.66, C:K.71, C:R.73, C:R.73, C:K.221, C:K.221, C:K.221 pi-Cation interactions: C:R.73

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 8 residues within 4Å: Chain C: L.93, V.382 Chain D: Q.35, W.36, P.37, P.145, S.146, N.149 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:L.93, D:W.36, D:S.146, D:S.146, D:N.149

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: C
p51 RT: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

D
B

Reverse transcriptase/ribonuclease H

p51 RT

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