1VRT

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.186 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


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

  • DOI: 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 ...

    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.

    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
    Organizational Affiliation: 

    Laboratory of Molecular Biophysics, Oxford, UK.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HIV-1 REVERSE TRANSCRIPTASEA560Human immunodeficiency virus 1Mutation(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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HIV-1 REVERSE TRANSCRIPTASEB440Human immunodeficiency virus 1Mutation(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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NVP (Subject of Investigation/LOI)
Query on NVP
Download Ideal Coordinates CCD File 
D [auth A]11-CYCLOPROPYL-5,11-DIHYDRO-4-METHYL-6H-DIPYRIDO[3,2-B:2',3'-E][1,4]DIAZEPIN-6-ONE
C15 H14 N4 O
NQDJXKOVJZTUJA-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSD
Query on CSD		AL-PEPTIDE LINKINGC3 H7 N O4 SCYS
Binding Affinity Annotations 
IDSourceBinding Affinity
NEV BindingDB:  1VRT Ki: min: 400, max: 3.60e+4 (nM) from 8 assay(s)
IC50: min: 2.6, max: 2.30e+4 (nM) from 51 assay(s)
EC50: min: 20, max: 7500 (nM) from 12 assay(s)
PDBBind:  1VRT IC50: 80 (nM) from 1 assay(s)
NVP Binding MOAD:  1VRT IC50: 80 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.186 
  • R-Value Observed: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.8α = 90
b = 116.7β = 90
c = 66.4γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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