1LWF | pdb_00001lwf

CRYSTAL STRUCTURE OF A MUTANT HIV-1 REVERSE TRANSCRIPTASE (RTMQ+M184V: M41L/D67N/K70R/M184V/T215Y) IN COMPLEX WITH NEVIRAPINE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.289 (Depositor) 
  • R-Value Work: 
    0.234 (Depositor), 0.213 (DCC) 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 

Literature

Crystal structures of Zidovudine- or Lamivudine-resistant human immunodeficiency virus type 1 reverse transcriptases containing mutations at codons 41, 184, and 215.

Chamberlain, P.P., Ren, J., Nichols, C.E., Douglas, L., Lennerstrand, J., Larder, B.A., Stuart, D.I., Stammers, D.K.

(2002) J Virol 76: 10015-10019

  • DOI: https://doi.org/10.1128/jvi.76.19.10015-10019.2002
  • Primary Citation Related Structures: 
    1LW0, 1LW2, 1LWC, 1LWE, 1LWF

  • PubMed Abstract: 

    Six structures of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) containing combinations of resistance mutations for zidovudine (AZT) (M41L and T215Y) or lamivudine (M184V) have been determined as inhibitor complexes. Minimal conformational changes in the polymerase or nonnucleoside RT inhibitor sites compared to the mutant RTMC (D67N, K70R, T215F, and K219N) are observed, indicating that such changes may occur only with certain combinations of mutations. Model building M41L and T215Y into HIV-1 RT-DNA and docking in ATP that is utilized in the pyrophosphorolysis reaction for AZT resistance indicates that some conformational rearrangement appears necessary in RT for ATP to interact simultaneously with the M41L and T215Y mutations.

    • Organizational Affiliation: 
    • Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 116.34 kDa 
  • Atom Count: 7,729 
  • Modeled Residue Count: 938 
  • Deposited Residue Count: 1,000 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HIV-1 REVERSE TRANSCRIPTASE560Human immunodeficiency virus 1Mutation(s): 6 
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 Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04585
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
HIV-1 REVERSE TRANSCRIPTASE440Human immunodeficiency virus 1Mutation(s): 5 
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 Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04585
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NVP

Query on NVP


Download:Ideal Coordinates CCD File
C [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
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSD
Query on CSD
A
L-PEPTIDE LINKINGC3 H7 N O4 SCYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.289 (Depositor) 
  • R-Value Work:  0.234 (Depositor), 0.213 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.9α = 90
b = 109.5β = 90
c = 74.1γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-10-30
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-11-13
    Changes: Data collection, Structure summary