6O9E | pdb_00006o9e

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

PDB DOI: https://doi.org/10.2210/pdb6O9E/pdb
NAKB: 6O9E

Classification: TRANSFERASE/DNA
Organism(s): Human immunodeficiency virus 1, synthetic construct
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2019-03-13 Released: 2019-10-23
Deposition Author(s): Ruiz, F.X., Hoang, A., Das, K., Arnold, E.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.242 (Depositor), 0.249 (DCC)
R-Value Work:
0.203 (Depositor), 0.210 (DCC)
R-Value Observed:
0.204 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

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

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

(2019) J Med Chem 62: 9996-10002

PubMed: 31603676 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acs.jmedchem.9b01289
Primary Citation Related Structures:
6O9E

PubMed Abstract:
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.

Organizational Affiliation

Rega Institute for Medical Research , 3000 Leuven , Belgium.

Macromolecule Content

Total Structure Weight: 254.1 kDa
Atom Count: 17,583
Modeled Residue Count: 2,001
Deposited Residue Count: 2,044
Unique protein chains: 2
Unique nucleic acid chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reverse transcriptase p66	A, C	555	Human immunodeficiency virus 1	Mutation(s): 2 EC: 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.13 (PDB Primary Data)
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03366 Go to UniProtKB: P03366
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03366
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Reverse transcriptase p51	B, D	429	Human immunodeficiency virus 1	Mutation(s): 1 EC: 3.4.23.16
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03366 Go to UniProtKB: P03366
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03366
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 3
DNA (38-MER)	E [auth F], F [auth E]	38	synthetic construct
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	G, H	2		N/A	Interactions Focus chain G Focus chain H Interactions & Density Focus chain G Focus chain H
Glycosylation Resources
GlyTouCan: G05551OP GlyCosmos: G05551OP

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IY1 (Subject of Investigation/LOI) Query on IY1 Download:Ideal Coordinates CCD File SDF format, chain X [auth E] SDF format, chain V [auth F] MOL2 format, chain X [auth E] MOL2 format, chain V [auth F] mmCIF format, chain X [auth E] mmCIF format, chain V [auth F]	V [auth F], X [auth E]	5-methyl-1-(4-nitrophenyl)-2-oxo-2,5-dihydro-1H-pyrido[3,2-b]indole-3-carbonitrile C₁₉ H₁₂ N₄ O₃ TZEXGCXFOXXFKH-UHFFFAOYSA-N		Interactions Focus chain V [auth F] Focus chain X [auth E] Interactions & Density Focus chain V [auth F] Focus chain X [auth E]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain W [auth E] MOL2 format, chain W [auth E] mmCIF format, chain W [auth E]	W [auth E]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain W [auth E] Interactions & Density Focus chain W [auth E]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B]	P [auth B], Q [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain P [auth B] Focus chain Q [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A] J [auth A] L [auth B] M [auth B] R [auth C] I [auth A], J [auth A], L [auth B], M [auth B], R [auth C], S [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain R [auth C] Focus chain S [auth C] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain R [auth C] Focus chain S [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain T [auth C] SDF format, chain O [auth B] SDF format, chain N [auth B] MOL2 format, chain T [auth C] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] mmCIF format, chain T [auth C] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B]	N [auth B], O [auth B], T [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Focus chain O [auth B] Focus chain T [auth C] Interactions & Density Focus chain N [auth B] Focus chain O [auth B] Focus chain T [auth C]
NH4 Query on NH4 Download:Ideal Coordinates CCD File SDF format, chain U [auth C] SDF format, chain K [auth A] MOL2 format, chain U [auth C] MOL2 format, chain K [auth A] mmCIF format, chain U [auth C] mmCIF format, chain K [auth A]	K [auth A], U [auth C]	AMMONIUM ION H₄ N QGZKDVFQNNGYKY-UHFFFAOYSA-O		Interactions Focus chain K [auth A] Focus chain U [auth C] Interactions & Density Focus chain K [auth A] Focus chain U [auth C]

Binding Affinity Annotations
ID	Source	Binding Affinity
IY1	BindingDB: 6O9E	IC50: min: 19.7, max: 1123 (nM) from 3 assay(s)

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003 Query on PRD_900003	G, H	sucrose	Oligosaccharide / Nutrient		Interactions Focus chain G Focus chain H Interactions & Density Focus chain G Focus chain H

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.242 (Depositor), 0.249 (DCC)
R-Value Work: 0.203 (Depositor), 0.210 (DCC)
R-Value Observed: 0.204 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.762	α = 90
b = 127.663	β = 101.5
c = 131.61	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-10-23

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	MERIT Award R37 AI027690

Revision History (Full details and data files)

Version 1.0: 2019-10-23
Type: Initial release
Version 1.1: 2019-11-06
Changes: Data collection, Database references
Version 1.2: 2019-11-27
Changes: Database references
Version 1.3: 2020-01-01
Changes: Author supporting evidence
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-10-11
Changes: Data collection, Database references, Refinement description, Structure summary