2HNY

Crystal Structure of E138K Mutant HIV-1 Reverse Transcriptase in Complex with Nevirapine

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 

wwPDB Validation 3D Report Full Report


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


Literature

Structural insights into mechanisms of non-nucleoside drug resistance for HIV-1 reverse transcriptases mutated at codons 101 or 138.

Ren, J., Nichols, C.E., Stamp, A., Chamberlain, P.P., Ferris, R., Weaver, K.L., Short, S.A., Stammers, D.K.

(2006) FEBS J 273: 3850-3860

  • DOI: 10.1111/j.1742-4658.2006.05392.x
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • Lys101Glu is a drug resistance mutation in reverse transcriptase clinically observed in HIV-1 from infected patients treated with the non-nucleoside inhibitor (NNRTI) drugs nevirapine and efavirenz. In contrast to many NNRTI resistance mutations, Lys ...

    Lys101Glu is a drug resistance mutation in reverse transcriptase clinically observed in HIV-1 from infected patients treated with the non-nucleoside inhibitor (NNRTI) drugs nevirapine and efavirenz. In contrast to many NNRTI resistance mutations, Lys101(p66 subunit) is positioned at the surface of the NNRTI pocket where it interacts across the reverse transcriptase (RT) subunit interface with Glu138(p51 subunit). However, nevirapine contacts Lys101 and Glu138 only indirectly, via water molecules, thus the structural basis of drug resistance induced by Lys101Glu is unclear. We have determined crystal structures of RT(Glu138Lys) and RT(Lys101Glu) in complexes with nevirapine to 2.5 A, allowing the determination of water structure within the NNRTI-binding pocket, essential for an understanding of nevirapine binding. Both RT(Glu138Lys) and RT(Lys101Glu) have remarkably similar protein conformations to wild-type RT, except for significant movement of the mutated side-chains away from the NNRTI pocket induced by charge inversion. There are also small shifts in the position of nevirapine for both mutant structures which may influence ring stacking interactions with Tyr181. However, the reduction in hydrogen bonds in the drug-water-side-chain network resulting from the mutated side-chain movement appears to be the most significant contribution to nevirapine resistance for RT(Lys101Glu). The movement of Glu101 away from the NNRTI pocket can also explain the resistance of RT(Lys101Glu) to efavirenz but in this case is due to a loss of side-chain contacts with the drug. RT(Lys101Glu) is thus a distinctive NNRTI resistance mutant in that it can give rise to both direct and indirect mechanisms of drug resistance, which are inhibitor-dependent.

    Organizational Affiliation: 

    Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, Henry Wellcome Building for Genomic Medicine, University of Oxford, UK.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Reverse transcriptase/ribonuclease H
B
422Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: 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 P03367 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI))
Go to UniProtKB:  P03367
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Reverse transcriptase/ribonuclease H
A
534Human immunodeficiency virus 1Mutation(s): 2 
Gene Names: 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))
Go to UniProtKB:  P04585
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 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
PO4
Query on PO4
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 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:  23000   nM  BindingDB
NEVIC50:  84   nM  BindingDB
NEVIC50:  2600   nM  BindingDB
NEVKi:  36000   nM  BindingDB
NEVEC50:  250   nM  BindingDB
NEVIC50:  101   nM  BindingDB
NEVIC50:  100   nM  BindingDB
NEVIC50:  1900   nM  BindingDB
NEVEC50:  380   nM  BindingDB
NEVIC50:  1700   nM  BindingDB
NEVIC50:  11300   nM  BindingDB
NEVIC50:  11800   nM  BindingDB
NEVKi:  18000   nM  BindingDB
NEVIC50:  13000   nM  BindingDB
NEVIC50:  14000   nM  BindingDB
NEVIC50:  60   nM  BindingDB
NEVIC50:  690   nM  BindingDB
NEVIC50:  20000   nM  BindingDB
NEVIC50:  2.5999999046325684   nM  BindingDB
NEVIC50:  80   nM  BindingDB
NEVIC50:  5750   nM  BindingDB
NEVIC50:  5500   nM  BindingDB
NEVIC50:  6000   nM  BindingDB
NEVIC50:  6650   nM  BindingDB
NEVIC50:  6440   nM  BindingDB
NEVIC50:  2800   nM  BindingDB
NEVIC50:  3100   nM  BindingDB
NEVIC50:  3000   nM  BindingDB
NEVIC50:  3200   nM  BindingDB
NEVIC50:  3500   nM  BindingDB
NVPIC50:  1165   nM  Binding MOAD
NEVIC50:  3800   nM  BindingDB
NEVIC50:  3930   nM  BindingDB
NEVKi:  400   nM  BindingDB
NEVIC50:  4848   nM  BindingDB
NEVEC50:  7500   nM  BindingDB
NEVIC50:  1480   nM  BindingDB
NEVEC50:  20   nM  BindingDB
NEVEC50:  3900   nM  BindingDB
NEVKi:  2000   nM  BindingDB
NEVIC50:  1900   nM  BindingDB
NEVIC50:  1850   nM  BindingDB
NEVEC50:  26   nM  BindingDB
NEVIC50:  2110   nM  BindingDB
NEVIC50:  700   nM  BindingDB
NEVIC50:  80   nM  BindingDB
NEVIC50:  84   nM  BindingDB
NEVIC50:  860   nM  BindingDB
NEVIC50:  1100   nM  BindingDB
NEVIC50:  1300   nM  BindingDB
NEVKi:  7000   nM  BindingDB
NEVKi:  9000   nM  BindingDB
NEVEC50:  70   nM  BindingDB
NEVIC50:  430   nM  BindingDB
NEVEC50:  110   nM  BindingDB
NEVKi:  10000   nM  BindingDB
NEVIC50:  500   nM  BindingDB
NEVIC50:  640   nM  BindingDB
NEVEC50:  100   nM  BindingDB
NEVIC50:  600   nM  BindingDB
NEVIC50:  180   nM  BindingDB
NVPIC50 :  1165   nM  PDBBind
NEVIC50:  170   nM  BindingDB
NEVIC50:  200   nM  BindingDB
NEVEC50:  30   nM  BindingDB
NEVIC50:  230   nM  BindingDB
NEVEC50:  52   nM  BindingDB
NEVEC50:  53   nM  BindingDB
NEVIC50:  250   nM  BindingDB
NEVIC50:  270   nM  BindingDB
NEVIC50:  320   nM  BindingDB
NEVIC50:  300   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.6α = 90
b = 115β = 90
c = 65.6γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-09-05
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance