Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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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: 116284.60 
• Atom Count: 7648 
• Residue Count: 1000 
• Unique protein chains: 2

1VRT

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

• DOI: 10.2210/pdb1VRT/pdb

• Classification: NUCLEOTIDYLTRANSFERASE
• Organism(s): Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)
• Expression System: Escherichia coli


• Deposited: 1995-04-19 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: 2.2 Å
• R-Value Work: 0.186 

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.Mol.Biol. 2: 293-302

• PubMed: 7540934 
• Primary Citation of Related Structures:  
  1VRU, 1RTI, 1RTH
• Also Cited By: 3V81, 1DTT, 1DTQ


• 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.Mol.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.

Macromolecules

Find similar proteins by: Sequence  |  Structure

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

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NVP	A	11-CYCLOPROPYL-5,11-DIHYDRO-4-METHYL-6H-DIPYRIDO[3,2-B:2',3'-E][1,4]DIAZEPIN-6-ONE NON-NUCLEOSIDE RT INHIBITOR NEVIRAPINE C15 H14 N4 O NQDJXKOVJZTUJA-UHFFFAOYSA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
NVP	IC50: 80 nM BINDINGMOAD
NEV	IC50: 80 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Work: 0.186 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 141.800	α = 90.00
b = 116.700	β = 90.00
c = 66.400	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1995-04-19 
• 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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance