7LRY | pdb_00007lry

Structure of HIV-1 Reverse Transcriptase in complex with DNA, (-)FTC-TP, and CA(2+) ion

PDB DOI: https://doi.org/10.2210/pdb7LRY/pdb
NAKB: 7LRY

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

Deposited: 2021-02-17 Released: 2022-02-23
Deposition Author(s): Hoang, A., Ruiz, F.X., Arnold, E.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.222 (Depositor), 0.230 (DCC)
R-Value Work:
0.190 (Depositor), 0.198 (DCC)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structural basis of HIV inhibition by L-nucleosides: Opportunities for drug development and repurposing.

Ruiz, F.X., Hoang, A., Dilmore, C.R., DeStefano, J.J., Arnold, E.

(2022) Drug Discov Today 27: 1832-1846

PubMed: 35218925 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.drudis.2022.02.016
Primary Citation Related Structures:
7LRI, 7LRM, 7LRX, 7LRY, 7LSK

PubMed Abstract:
Infection with HIV can cripple the immune system and lead to AIDS. Hepatitis B virus (HBV) is a hepadnavirus that causes human liver diseases. Both pathogens are major public health problems affecting millions of people worldwide. The polymerases from both viruses are the most common drug target for viral inhibition, sharing common architecture at their active sites. The L-nucleoside drugs emtricitabine and lamivudine are widely used HIV reverse transcriptase (RT) and HBV polymerase (Pol) inhibitors. Nevertheless, structural details of their binding to RT(Pol)/nucleic acid remained unknown until recently. Here, we discuss the implications of these structures, alongside related complexes with L-dNTPs, for the development of novel L-nucleos(t)ide drugs, and prospects for repurposing them.

Organizational Affiliation

Center for Advanced Biotechnology and Medicine, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA. Electronic address: xavier@cabm.rutgers.edu.

Macromolecule Content

Total Structure Weight: 254.83 kDa
Atom Count: 17,803
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
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/RNA (38-MER)	E [auth F], F [auth E]	38	synthetic construct
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1RY (Subject of Investigation/LOI) Query on 1RY Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain Y [auth C] MOL2 format, chain N [auth A] MOL2 format, chain Y [auth C] mmCIF format, chain N [auth A] mmCIF format, chain Y [auth C]	N [auth A], Y [auth C]	[[(2R,5S)-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate C₈ H₁₃ F N₃ O₁₂ P₃ S WIEOLFZNMKSGEX-NTSWFWBYSA-N		Interactions Focus chain N [auth A] Focus chain Y [auth C] Interactions & Density Focus chain N [auth A] Focus chain Y [auth C]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain T [auth B] SDF format, chain V [auth C] MOL2 format, chain I [auth A] MOL2 format, chain T [auth B] MOL2 format, chain V [auth C] mmCIF format, chain I [auth A] mmCIF format, chain T [auth B] mmCIF format, chain V [auth C]	I [auth A], T [auth B], V [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain T [auth B] Focus chain V [auth C] Interactions & Density Focus chain I [auth A] Focus chain T [auth B] Focus chain V [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth F] SDF format, chain J [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain U [auth B] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain U [auth B] MOL2 format, chain Z [auth D] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth F] mmCIF format, chain J [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain U [auth B] mmCIF format, chain Z [auth D]	AA [auth D] BA [auth D] CA [auth D] DA [auth F] J [auth A] AA [auth D], BA [auth D], CA [auth D], DA [auth F], J [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], U [auth B], Z [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth F] Focus chain J [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain U [auth B] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth F] Focus chain J [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain U [auth B] Focus chain Z [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain X [auth C] MOL2 format, chain M [auth A] MOL2 format, chain X [auth C] mmCIF format, chain M [auth A] mmCIF format, chain X [auth C]	M [auth A], X [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain X [auth C] Interactions & Density Focus chain M [auth A] Focus chain X [auth C]
NH4 Query on NH4 Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain W [auth C] MOL2 format, chain L [auth A] MOL2 format, chain W [auth C] mmCIF format, chain L [auth A] mmCIF format, chain W [auth C]	L [auth A], W [auth C]	AMMONIUM ION H₄ N QGZKDVFQNNGYKY-UHFFFAOYSA-O		Interactions Focus chain L [auth A] Focus chain W [auth C] Interactions & Density Focus chain L [auth A] Focus chain W [auth C]