1RTJ | pdb_00001rtj

MECHANISM OF INHIBITION OF HIV-1 REVERSE TRANSCRIPTASE BY NON-NUCLEOSIDE INHIBITORS

• PDB DOI: https://doi.org/10.2210/pdb1RTJ/pdb

• Classification: NUCLEOTIDYLTRANSFERASE
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1995-05-03 Released: 1996-04-03 
• Deposition Author(s): Ren, J., Esnouf, R., Ross, C., Jones, Y., Stammers, D., Stuart, D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Work: 
  0.219 (Depositor) 
• R-Value Observed: 
  0.219 (Depositor) 

Literature

Mechanism of inhibition of HIV-1 reverse transcriptase by non-nucleoside inhibitors.

Esnouf, R., Ren, J., Ross, C., Jones, Y., Stammers, D., Stuart, D.

(1995) Nat Struct Biol 2: 303-308

• PubMed: 7540935 
• DOI: https://doi.org/10.1038/nsb0495-303
• Primary Citation Related Structures: 
  1RTJ


• PubMed Abstract: 
  

  The structure of unliganded HIV-1 reverse transcriptase has been determined at 2.35 A resolution and refined to an R-factor of 0.219 (for all data) with good stereochemistry. The unliganded structure was produced by soaking out a weak binding non-nucleoside inhibitor, HEPT, from pregrown crystals. Comparison with the structures of four different RT and non-nucleoside inhibitor complexes reveals that only minor domain rearrangements occur, but there is a significant repositioning of a three-stranded beta-sheet in the p66 subunit (containing the catalytic aspartic acid residues 110, 185 and 186) with respect to the rest of the polymerase site. This suggests that NNIs inhibit RT by locking the polymerase active site in an inactive conformation, reminiscent of the conformation observed in the inactive p51 subunit.

---

Organizational Affiliation: 
• Laboratory of Molecular Biophysics, Oxford, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 115.99 kDa 
• Atom Count: 8,210 
• Modeled Residue Count: 969 
• Deposited Residue Count: 1,000 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 REVERSE TRANSCRIPTASE	A	560	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: HIV-1 POL EC: 2.7.7.49
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04585  Go to UniProtKB:  P04585

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 REVERSE TRANSCRIPTASE	B	440	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: HIV-1 POL EC: 2.7.7.49
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04585  Go to UniProtKB:  P04585

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Work:  0.219 (Depositor) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.5	α = 90
b = 109.4	β = 90
c = 72.3	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-04-03 
Deposition Author(s): Ren, J., Esnouf, R., Ross, C., Jones, Y., Stammers, D., Stuart, D.

Revision History  

• Version 1.0: 1996-04-03
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-06-05
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.4: 2024-10-23
  Changes: Structure summary