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:  
    1VRT, 1VRU, 1RTI, 1RTH

  • 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 ...

    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)
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Explore P04585 
Go to UniProtKB:  P04585
Protein Feature View
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  • 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)
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
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NVP
Query on NVP

Download CCD File 
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 CCD File 
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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NEVIC50:  100   nM  BindingDB
NEVIC50:  1480   nM  BindingDB
NEVIC50:  14000   nM  BindingDB
NEVEC50:  26   nM  BindingDB
NEVIC50:  1300   nM  BindingDB
NEVIC50:  1100   nM  BindingDB
NEVEC50:  30   nM  BindingDB
NEVEC50:  7500   nM  BindingDB
NEVIC50:  860   nM  BindingDB
NEVIC50:  700   nM  BindingDB
NEVEC50:  52   nM  BindingDB
NEVEC50:  53   nM  BindingDB
NEVIC50:  640   nM  BindingDB
NEVIC50:  600   nM  BindingDB
NEVKi:  7000   nM  BindingDB
NEVIC50:  500   nM  BindingDB
NEVKi:  9000   nM  BindingDB
NEVEC50:  70   nM  BindingDB
NEVIC50:  430   nM  BindingDB
NEVIC50:  2.5999999046325684   nM  BindingDB
NEVIC50:  320   nM  BindingDB
NEVIC50:  300   nM  BindingDB
NEVIC50:  270   nM  BindingDB
NEVIC50:  250   nM  BindingDB
NEVIC50:  300   nM  BindingDB
NEVIC50:  230   nM  BindingDB
NEVIC50:  200   nM  BindingDB
NEVIC50:  180   nM  BindingDB
NEVIC50:  170   nM  BindingDB
NEVEC50:  3900   nM  BindingDB
NEVIC50:  80   nM  BindingDB
NEVEC50:  20   nM  BindingDB
NEVKi:  2000   nM  BindingDB
NEVEC50:  380   nM  BindingDB
NEVIC50:  101   nM  BindingDB
NEVIC50:  23000   nM  BindingDB
NEVIC50:  84   nM  BindingDB
NEVIC50:  80   nM  BindingDB
NEVIC50:  1900   nM  BindingDB
NEVIC50:  2600   nM  BindingDB
NEVIC50:  60   nM  BindingDB
NEVIC50:  13000   nM  BindingDB
NEVIC50:  11800   nM  BindingDB
NEVIC50:  11300   nM  BindingDB
NEVKi:  400   nM  BindingDB
NEVIC50 :  80   nM  PDBBind
NVPIC50:  80   nM  Binding MOAD
NEVKi:  10000   nM  BindingDB
NEVIC50:  6650   nM  BindingDB
NEVIC50:  6440   nM  BindingDB
NEVIC50:  6000   nM  BindingDB
NEVIC50:  5750   nM  BindingDB
NEVEC50:  110   nM  BindingDB
NEVIC50:  5500   nM  BindingDB
NEVEC50:  100   nM  BindingDB
NEVIC50:  4848   nM  BindingDB
NEVKi:  400   nM  BindingDB
NEVIC50:  3930   nM  BindingDB
NEVIC50:  3800   nM  BindingDB
NEVKi:  18000   nM  BindingDB
NEVIC50:  690   nM  BindingDB
NEVIC50:  3500   nM  BindingDB
NEVIC50:  20000   nM  BindingDB
NEVIC50:  3200   nM  BindingDB
NEVIC50:  3100   nM  BindingDB
NEVIC50:  3000   nM  BindingDB
NEVIC50:  2800   nM  BindingDB
NEVIC50:  1700   nM  BindingDB
NEVEC50:  250   nM  BindingDB
NEVIC50:  2110   nM  BindingDB
NEVIC50:  1900   nM  BindingDB
NEVIC50:  1850   nM  BindingDB
NEVKi:  36000   nM  BindingDB
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

View Full Validation Report



Entry History 

Deposition Data

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