7TAZ | pdb_00007taz

Crystal structure of HIV-1 reverse transcriptase (RT) in complex with VM-1500A, a non-nucleoside RT inhibitor

• PDB DOI: https://doi.org/10.2210/pdb7TAZ/pdb

• Classification: TRANSFERASE/INHIBITOR
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2021-12-21 Released: 2023-04-12 
• Deposition Author(s): Snyder, A.A., Risener, C.J., Kirby, K.A., Sarafianos, S.G.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.279 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.247 (Depositor), 0.249 (DCC) 
• R-Value Observed: 
  0.249 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of HIV-1 reverse transcriptase (RT) in complex with VM-1500A, a non-nucleoside RT inhibitor

Snyder, A.A., Risener, C.J., Kirby, K.A., Stefan, S.G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 114.66 kDa 
• Atom Count: 7,804 
• Modeled Residue Count: 934 
• Deposited Residue Count: 986 
• Unique protein chains: 2

Macromolecules

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), 3.1.13.2 (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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Reverse transcriptase p51	B	429	Human immunodeficiency virus 1	Mutation(s): 1  EC: 2.7.7.49
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03366  Go to UniProtKB:  P03366

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VM5 (Subject of Investigation/LOI)	C [auth A]	2-[4-bromo-3-(3-chloro-5-cyanophenoxy)-2-fluorophenyl]-N-(2-chloro-4-sulfamoylphenyl)acetamide C21 H13 Br Cl2 F N3 O4 S SBUUICLVCQQMFP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.279 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.247 (Depositor), 0.249 (DCC) 
• R-Value Observed: 0.249 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 163.05	α = 90
b = 73.87	β = 99.96
c = 108.64	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-04-12 
Deposition Author(s): Snyder, A.A., Risener, C.J., Kirby, K.A., Sarafianos, S.G.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R37-AI076119

Revision History  

• Version 1.0: 2023-04-12
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description
• Version 2.0: 2026-04-29
  Type: Coordinate replacement
  Reason: Atoms with unrealistic or zero occupancies
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Refinement description, Structure summary