1RTH

HIGH RESOLUTION STRUCTURES OF HIV-1 RT FROM FOUR RT-INHIBITOR COMPLEXES

• PDB DOI:  https://doi.org/10.2210/pdb1RTH/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., Garman, E., Somers, D., Ross, C., Kirby, I., Keeling, J., Darby, G., Jones, Y., Stuart, D., Stammers, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Work: 0.214 
• R-Value Observed: 0.214 

Literature

High resolution structures of HIV-1 RT from four RT-inhibitor complexes.

Ren, J., Esnouf, R., Garman, E., Somers, D., Ross, C., Kirby, I., Keeling, J., Darby, G., Jones, Y., Stuart, D.

(1995) Nat Struct Biol 2: 293-302

• PubMed: 7540934 
• DOI: https://doi.org/10.1038/nsb0495-293
• Primary Citation of Related Structures:  
  1RTH, 1RTI, 1VRT, 1VRU


• PubMed Abstract: 
  

We have determined the structures of four complexes of HIV-1 reverse transcriptase with non-nucleoside inhibitors, three fully refined at high resolution. The highest resolution structure is of the RT-nevirapine complex which has an R-factor of 0.186 and a root-mean-square bond length deviation of 0.015 A for all data to 2.2 A. The structures reveal a common mode of binding for these chemically diverse compounds. The common features of binding are largely hydrophobic interactions and arise from induced shape complementarity achieved by conformational rearrangement of the enzyme and conformational/configurational rearrangement of the compounds.

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Related Citations: 

• 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

• Crystals of HIV-1 Reverse Transcriptase Diffracting to 2.2 Angstrom Resolution
  Stammers, D.K., Somers, D., Ross, C.K., Kirby, I., Ray, P.H., Wilson, J.E., Norman, M., Ren, J.S., Esnouf, R.M., Garman, E.F., Jones, E.Y., Stuart, D.I.
  (1994) J Mol Biol 242: 586

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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: 116.29 kDa 
• Atom Count: 8,146 
• Modelled Residue Count: 963 
• 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 (PDB Primary Data), 3.4.23.16 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
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 (PDB Primary Data), 3.4.23.16 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04585  Go to UniProtKB:  P04585

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U05	C [auth A]	6,11-DIHYDRO-11-ETHYL-6-METHYL-9-NITRO-5H-PYRIDO[2,3-B][1,5]BENZODIAZEPIN-5-ONE C15 H14 N4 O3 YCFJZPGDTZVVSM-UHFFFAOYSA-N

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

Binding Affinity Annotations
ID	Source	Binding Affinity
U05	PDBBind:  1RTH	IC50: 400 (nM) from 1 assay(s)
	BindingDB:  1RTH	IC50: 400 (nM) from 1 assay(s)
	Binding MOAD:  1RTH	IC50: 400 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Work: 0.214 
• R-Value Observed: 0.214 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.1	α = 90
b = 110.9	β = 90
c = 73.3	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., Garman, E., Somers, D., Ross, C., Kirby, I., Keeling, J., Darby, G., Jones, Y., Stuart, D., Stammers, 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