8VUB | pdb_00008vub

Crystal structure of wild-type HIV-1 reverse transcriptase in complex with non-nucleoside inhibitor 5e2

PDB DOI: https://doi.org/10.2210/pdb8VUB/pdb

Classification: VIRAL PROTEIN,TRANSFERASE/INHIBITOR
Organism(s): Human immunodeficiency virus 1
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-01-29 Released: 2025-04-30
Deposition Author(s): Rumrill, S., Ruiz, F.X., Arnold, E.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.18 Å
R-Value Free:
0.242 (Depositor), 0.244 (DCC)
R-Value Work:
0.199 (Depositor), 0.199 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Diarylpyrimidine-evolved HIV-1 non-nucleoside reverse transcriptase inhibitors show improved resistance and pharmacokinetic profiles against highly drug-resistant strains

Wang, Z., Rumrill, S.R., Kang, D., Desta, S., Feng, D., De Clercq, E., Pannecouque, C., Chen, C.H., Arnold, E., Ruiz, F.X., Liu, X., Zhan, P.

To be published.

Macromolecule Content

Total Structure Weight: 115.51 kDa
Atom Count: 8,720
Modelled Residue Count: 970
Deposited Residue Count: 985
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reverse transcriptase/ribonuclease H	A	557	Human immunodeficiency virus 1	Mutation(s): 3 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03366
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
p51 RT	B	428	Human immunodeficiency virus 1	Mutation(s): 1 Gene Names: gag-pol
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03366
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PKX (Subject of Investigation/LOI) Query on PKX Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	4-[(4-{[4-(4-cyano-2,6-dimethylphenoxy)-6,7-dimethoxyquinazolin-2-yl]amino}piperidin-1-yl)methyl]benzamide C₃₂ H₃₄ N₆ O₄ AYMBEDDCWNANIW-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	D [auth A] E [auth A] F [auth A] G [auth A] K [auth B] D [auth A], E [auth A], F [auth A], G [auth A], K [auth B], L [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B]	H [auth A], I [auth A], M [auth B], N [auth B], O [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.18 Å
R-Value Free: 0.242 (Depositor), 0.244 (DCC)
R-Value Work: 0.199 (Depositor), 0.199 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 162.845	α = 90
b = 72.523	β = 99.98
c = 109.236	γ = 90

Software Package:

Software Name	Purpose
Coot	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-04-30

Deposition Author(s):

Rumrill, S.

Ruiz, F.X.

Arnold, E.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI027690
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM008339
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM135141

Revision History (Full details and data files)

Version 1.0: 2025-04-30
Type: Initial release

Prepare Data

Validate Data

Deposit Data

Help and Resources

.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 8VUB | pdb_00008vub

Crystal structure of wild-type HIV-1 reverse transcriptase in complex with non-nucleoside inhibitor 5e2

Diarylpyrimidine-evolved HIV-1 non-nucleoside reverse transcriptase inhibitors show improved resistance and pharmacokinetic profiles against highly drug-resistant strains

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2