ISDA

Deposition Date 2019-03-13

Release Date 2019-10-23

Last Version Date 2023-10-11

Entry Detail

PDB ID:

6O9E

Keywords:

TRANSFERASE/DNA

Title:

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

Biological Source:

Source Organism:

Human immunodeficiency virus type 1 (Taxon ID: 11676)
synthetic construct (Taxon ID: 32630)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.40 Å

R-Value Free:

0.24

R-Value Work:

0.20

R-Value Observed:

0.20

Space Group:

P 1 21 1

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Reverse transcriptase p66
Gene (Uniprot):gag-pol
Mutations:C280S, D498N
Chain IDs:A, C
Chain Length:555
Number of Molecules:2
Biological Source:Human immunodeficiency virus type 1

UniProt ID:P03366 Pfam ID:PF00078, PF06817, PF06815, PF00075 EC:3.1.26.13

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Reverse transcriptase p51
Gene (Uniprot):gag-pol
Mutations:C280S
Chain IDs:B, D
Chain Length:429
Number of Molecules:2
Biological Source:Human immunodeficiency virus type 1

UniProt ID:P03366 Pfam ID:PF00078, PF06817, PF06815, PF00075 EC:3.1.26.13

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (38-MER)
Chain IDs:E (auth: F), F (auth: E)
Chain Length:38
Number of Molecules:2
Biological Source:synthetic construct

Ligand Molecules

GOL

IY1

NH4

PEG

PG4

SO4

Peptide-like Molecules

PRD_900003

Primary Citation

Structural Basis of HIV-1 Inhibition by Nucleotide-Competing Reverse Transcriptase Inhibitor INDOPY-1.

Ruiz, F.X, Hoang, A, Das, K, Arnold, E.Show

J.Med.Chem. 62 9996 10002 (2019)

PMID: 31603676 DOI: 10.1021/acs.jmedchem.9b01289

Abstact

HIV-1 reverse transcriptase (RT) is an essential enzyme, targeting half of approved anti-AIDS drugs. While nucleoside RT inhibitors (NRTIs) are DNA chain terminators, the nucleotide-competing RT inhibitor (NcRTI) INDOPY-1 blocks dNTP binding to RT. Lack of structural information hindered INDOPY-1 improvement. Here we report the HIV-1 RT/DNA/INDOPY-1 crystal structure, revealing a unique mode of inhibitor binding at the polymerase active site without involving catalytic metal ions. The structure may enable new strategies for developing NcRTIs.

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Primary Citation of related structures