3MEG | pdb_00003meg

HIV-1 K103N Reverse Transcriptase in Complex with TMC278

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.289 (Depositor), 0.284 (DCC) 
  • R-Value Work: 
    0.229 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 
    0.232 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history. 

Literature

Crystal Structures of HIV-1 Reverse Transcriptase with Etravirine (TMC125) and Rilpivirine (TMC278): Implications for Drug Design.

Lansdon, E.B., Brendza, K.M., Hung, M., Wang, R., Mukund, S., Jin, D., Birkus, G., Kutty, N., Liu, X.

(2010) J Med Chem 53: 4295-4299

  • DOI: https://doi.org/10.1021/jm1002233
  • Primary Citation Related Structures: 
    3MEC, 3MED, 3MEE, 3MEG

  • PubMed Abstract: 

    Diarylpyrimidine (DAPY) non-nucleoside reverse transcriptase inhibitors (NNRTIs) have inherent flexibility, helping to maintain activity against a wide range of resistance mutations. Crystal structures were determined with wild-type and K103N HIV-1 reverse transcriptase with etravirine (TMC125) and rilpivirine (TMC278). These structures reveal a similar binding mode for TMC125 and TMC278, whether bound to wild-type or K103N RT. Comparison to previously published structures reveals differences in binding modes for TMC125 and differences in protein conformation for TMC278.

    • Organizational Affiliation: 
    • Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, California 94404, USA. eric.lansdon@gilead.com

Macromolecule Content 

  • Total Structure Weight: 116.78 kDa 
  • Atom Count: 7,903 
  • Modeled Residue Count: 956 
  • Deposited Residue Count: 1,000 
  • Unique protein chains: 2

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
p66 Reverse transcriptase560HIV-1 M:B_HXB2RMutation(s): 1 
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
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Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
p51 Reverse transcriptase440HIV-1 M:B_HXB2RMutation(s): 1 
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.289 (Depositor), 0.284 (DCC) 
  • R-Value Work:  0.229 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 0.232 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.583α = 90
b = 154.909β = 90
c = 153.722γ = 90
Software Package:
Software NamePurpose
BOSdata collection
AMoREphasing
CNXrefinement
HKL-2000data reduction
HKL-2000data scaling

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: 2010-05-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-07-18
    Changes: Non-polymer description
  • Version 1.3: 2015-06-17
    Changes: Non-polymer description
  • Version 1.4: 2021-10-06
    Changes: Database references, Derived calculations
  • Version 1.5: 2023-09-06
    Changes: Data collection, Refinement description