SMTL ID : 6o9e.2 (1 other biounit)

Structure of HIV-1 Reverse Transcriptase in complex with DNA and INDOPY-1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-1-1-mer

Ligands

1 x GLC- FRU: beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose(Non-covalent)

GLC-FRU.1: 9 residues within 4Å: Chain B: V.22, D.77, R.79, E.80, K.83, K.396, E.400, E.414, W.415 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.83, B:K.83, B:E.414, B:W.415, B:W.415, B:R.79, B:K.396

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

SO4.2: 5 residues within 4Å: Chain A: K.331, G.333, Q.334, G.335 Ligands: GOL.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.334, A:Q.334, A:G.335 Salt bridges: A:K.331 SO4.3: 3 residues within 4Å: Chain A: Q.278, K.281, Q.334 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.278 Salt bridges: A:K.281

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: W.426, D.511, I.526 Ligands: SO4.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.426

1 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.5: 5 residues within 4Å: Chain A: D.443, G.444, N.498, H.539, D.549 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.443, A:N.498

1 x IY1: 5-methyl-1-(4-nitrophenyl)-2-oxo-2,5-dihydro-1H-pyrido[3,2-b]indole-3-carbonitrile(Non-covalent)

IY1.6: 11 residues within 4Å: Chain A: R.72, A.114, Y.115, Q.151, G.152, F.160, M.184, D.185 Chain C: A.5, A.6, T.38 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Q.151 Hydrogen bonds: A:D.185 pi-Stacking: A:Y.115 pi-Cation interactions: A:R.72

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ruiz, F.X. et al., Structural Basis of HIV-1 Inhibition by Nucleotide-Competing Reverse Transcriptase Inhibitor INDOPY-1. J.Med.Chem. (2019)

Release Date

2019-10-23

Peptides

Reverse transcriptase p66: A
Reverse transcriptase p51: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Reverse transcriptase p66

Reverse transcriptase p51

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