1RL8

Crystal structure of the complex of resistant strain of hiv-1 protease(v82a mutant) with ritonavir


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of the complex of resistant strain of hiv-1 protease(v82a mutant) with ritonavir

Rezacova, P.Brynda, J.Sedlacek, J.Konvalinka, J.Fabry, M.Horejsi, M.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
protease RETROPEPSINA, B99Human immunodeficiency virus 1Mutation(s): 2 
Gene Names: gag-pol
EC: 3.4.23.16 (PDB Primary Data), 2.7.7.49 (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))
Explore P03367 
Go to UniProtKB:  P03367
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RIT
Query on RIT

Download CCD File 
A
RITONAVIR
C37 H48 N6 O5 S2
NCDNCNXCDXHOMX-XGKFQTDJSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001001 (RIT)
Query on PRD_001001
ARITONAVIRP /  Inhibitor

--

External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RIT-TΔS:  50.27000045776367   kJ/mol  BindingDB
RITKi:  15   nM  BindingDB
RITΔG:  42.63999938964844   kJ/mol  BindingDB
RITΔH:  51   kJ/mol  BindingDB
RIT-TΔS:  36.369998931884766   kJ/mol  BindingDB
RITΔG:  44.310001373291016   kJ/mol  BindingDB
RITΔG:  49.31999969482422   kJ/mol  BindingDB
RITΔG:  60.189998626708984   kJ/mol  BindingDB
RITΔH:  17.559999465942383   kJ/mol  BindingDB
RITΔH:  14.630000114440918   kJ/mol  BindingDB
RITΔG:  54.7599983215332   kJ/mol  BindingDB
RITKi:  23   nM  BindingDB
RIT-TΔS:  62.7599983215332   kJ/mol  BindingDB
RITΔG:  45.97999954223633   kJ/mol  BindingDB
RITΔG:  40.130001068115234   kJ/mol  BindingDB
RIT-TΔS:  51.0099983215332   kJ/mol  BindingDB
RITΔG:  55.18000030517578   kJ/mol  BindingDB
RIT-TΔS:  66.48999786376953   kJ/mol  BindingDB
RITΔH:  12.119999885559082   kJ/mol  BindingDB
RITΔH:  25.079999923706055   kJ/mol  BindingDB
RITKi:  0.3700000047683716   nM  BindingDB
RITKi:  60   nM  BindingDB
RITΔG:  44.72999954223633   kJ/mol  BindingDB
RITΔH:  15.050000190734863   kJ/mol  BindingDB
RIT-TΔS:  64.81999969482422   kJ/mol  BindingDB
RIT-TΔS:  44.75   kJ/mol  BindingDB
RITKi:  40   nM  BindingDB
RITΔH:  15.470000267028809   kJ/mol  BindingDB
RITΔG:  51.83000183105469   kJ/mol  BindingDB
RITKi:  0.05999999865889549   nM  BindingDB
RITΔG:  41.79999923706055   kJ/mol  BindingDB
RIT-TΔS:  33.040000915527344   kJ/mol  BindingDB
RITΔG:  35.529998779296875   kJ/mol  BindingDB
RITΔH:  26.75   kJ/mol  BindingDB
RIT-TΔS:  34.70000076293945   kJ/mol  BindingDB
RITΔH:  12.960000038146973   kJ/mol  BindingDB
RITΔG:  51.83000183105469   kJ/mol  BindingDB
RITΔH:  5.019999980926514   kJ/mol  BindingDB
RITΔH:  12.119999885559082   kJ/mol  BindingDB
RITΔG:  56.0099983215332   kJ/mol  BindingDB
RIT-TΔS:  60.63999938964844   kJ/mol  BindingDB
RITΔH:  15.470000267028809   kJ/mol  BindingDB
RIT-TΔS:  42.25   kJ/mol  BindingDB
RITKd:  0.6000000238418579   nM  BindingDB
RITΔG:  36.369998931884766   kJ/mol  BindingDB
RIT-TΔS:  58.59000015258789   kJ/mol  BindingDB
RITΔH:  40.130001068115234   kJ/mol  BindingDB
RIT-TΔS:  64.81999969482422   kJ/mol  BindingDB
RITΔG:  49.31999969482422   kJ/mol  BindingDB
RIT-TΔS:  76.94999694824219   kJ/mol  BindingDB
RITΔH:  40.130001068115234   kJ/mol  BindingDB
RITΔG:  45.13999938964844   kJ/mol  BindingDB
RITΔH:  22.56999969482422   kJ/mol  BindingDB
RIT-TΔS:  75.27999877929688   kJ/mol  BindingDB
RITΔG:  40.959999084472656   kJ/mol  BindingDB
RITΔG:  39.709999084472656   kJ/mol  BindingDB
RITKi:  30   nM  BindingDB
RITKi:  1.100000023841858   nM  BindingDB
RIT-TΔS:  42.63999938964844   kJ/mol  BindingDB
RITKi:  1.2000000476837158   nM  BindingDB
RITΔG:  53.5   kJ/mol  BindingDB
RITΔG:  53.5   kJ/mol  BindingDB
RIT-TΔS:  46.41999816894531   kJ/mol  BindingDB
RITΔG:  57.68000030517578   kJ/mol  BindingDB
RITΔG:  43.470001220703125   kJ/mol  BindingDB
RIT-TΔS:  43.91999816894531   kJ/mol  BindingDB
RITΔG:  56.43000030517578   kJ/mol  BindingDB
RIT-TΔS:  80.29000091552734   kJ/mol  BindingDB
RIT-TΔS:  79.04000091552734   kJ/mol  BindingDB
RIT-TΔS:  43.91999816894531   kJ/mol  BindingDB
RITΔG:  31.770000457763672   kJ/mol  BindingDB
RITΔH:  73.1500015258789   kJ/mol  BindingDB
RIT-TΔS:  58.560001373291016   kJ/mol  BindingDB
RITKi:  0.019999999552965164   nM  BindingDB
RIT-TΔS:  76.94999694824219   kJ/mol  BindingDB
RITKi:  109   nM  BindingDB
RITIC50:  67   nM  BindingDB
RITΔH:  0   kJ/mol  BindingDB
RITKi:  32   nM  BindingDB
RITΔG:  52.25   kJ/mol  BindingDB
RITΔG:  28.84000015258789   kJ/mol  BindingDB
RITΔH:  27.59000015258789   kJ/mol  BindingDB
RIT-TΔS:  43.08000183105469   kJ/mol  BindingDB
RITKi:  0.20000000298023224   nM  BindingDB
RITKi:  0.23000000417232513   nM  BindingDB
RITΔH:  11.699999809265137   kJ/mol  BindingDB
RITKi:  3.0999999046325684   nM  BindingDB
RITKi:  2.809999942779541   nM  BindingDB
RIT-TΔS:  76.54000091552734   kJ/mol  BindingDB
RITKi:  0.9100000262260437   nM  BindingDB
RITΔG:  54.34000015258789   kJ/mol  BindingDB
RITKi:  0.46000000834465027   nM  BindingDB
RITΔG:  50.15999984741211   kJ/mol  BindingDB
RITKi:  0.5899999737739563   nM  BindingDB
RITΔG:  38.040000915527344   kJ/mol  BindingDB
RITKi:  0.3700000047683716   nM  BindingDB
RITΔG:  33.439998626708984   kJ/mol  BindingDB
RITΔH:  21.739999771118164   kJ/mol  BindingDB
RITΔH:  13.789999961853027   kJ/mol  BindingDB
RITKi:  0.019999999552965164   nM  BindingDB
RITΔH:  43.470001220703125   kJ/mol  BindingDB
RITKi:  0.699999988079071   nM  BindingDB
RITΔH:  30.510000228881836   kJ/mol  BindingDB
RITKi:  13   nM  BindingDB
RITΔH:  35.95000076293945   kJ/mol  BindingDB
RITΔG:  38.869998931884766   kJ/mol  BindingDB
RIT-TΔS:  65.23999786376953   kJ/mol  BindingDB
RITKi:  2.4000000953674316   nM  BindingDB
RITKd:  0.6100000143051147   nM  BindingDB
RITΔG:  53.91999816894531   kJ/mol  BindingDB
RITΔH:  2.0899999141693115   kJ/mol  BindingDB
RIT-TΔS:  30.110000610351562   kJ/mol  BindingDB
RITKi:  0.699999988079071   nM  BindingDB
RIT-TΔS:  65.6500015258789   kJ/mol  BindingDB
RIT-TΔS:  45.59000015258789   kJ/mol  BindingDB
RITΔG:  52.66999816894531   kJ/mol  BindingDB
RITΔG:  36.779998779296875   kJ/mol  BindingDB
RITΔG:  34.279998779296875   kJ/mol  BindingDB
RIT-TΔS:  46.84000015258789   kJ/mol  BindingDB
RIT-TΔS:  102.05999755859375   kJ/mol  BindingDB
RITΔH:  12.960000038146973   kJ/mol  BindingDB
RITΔG:  45.560001373291016   kJ/mol  BindingDB
RITKi:  0.11999999731779099   nM  BindingDB
RIT-TΔS:  30.110000610351562   kJ/mol  BindingDB
RIT-TΔS:  57.33000183105469   kJ/mol  BindingDB
RITΔH:  4.599999904632568   kJ/mol  BindingDB
RITΔG:  49.7400016784668   kJ/mol  BindingDB
RITΔH:  12.539999961853027   kJ/mol  BindingDB
RIT-TΔS:  70.2699966430664   kJ/mol  BindingDB
RITKi:  0.5   nM  BindingDB
RIT-TΔS:  56.86000061035156   kJ/mol  BindingDB
RITKi:  0.05999999865889549   nM  BindingDB
RIT-TΔS:  57.29999923706055   kJ/mol  BindingDB
RITKi:  0.029999999329447746   nM  BindingDB
RITΔH:  9.609999656677246   kJ/mol  BindingDB
RITΔH:  12.119999885559082   kJ/mol  BindingDB
RITΔH:  2.930000066757202   kJ/mol  BindingDB
RITΔG:  45.560001373291016   kJ/mol  BindingDB
RITΔH:  12.960000038146973   kJ/mol  BindingDB
RIT-TΔS:  39.29999923706055   kJ/mol  BindingDB
RIT-TΔS:  69.83000183105469   kJ/mol  BindingDB
RIT-TΔS:  52.68000030517578   kJ/mol  BindingDB
RITΔG:  55.59000015258789   kJ/mol  BindingDB
RITΔH:  0.07999999821186066   kJ/mol  BindingDB
RITKi:  0.15000000596046448   nM  BindingDB
RITΔH:  17.969999313354492   kJ/mol  BindingDB
RITKi:  3.0199999809265137   nM  BindingDB
RITKi:  4.5   nM  BindingDB
RITΔH:  24.239999771118164   kJ/mol  BindingDB
RITKi:  4   nM  BindingDB
RITΔH:  10.869999885559082   kJ/mol  BindingDB
RIT-TΔS:  82.80000305175781   kJ/mol  BindingDB
RITΔH:  8.779999732971191   kJ/mol  BindingDB
RITΔH:  33.439998626708984   kJ/mol  BindingDB
RIT-TΔS:  35.540000915527344   kJ/mol  BindingDB
RITΔG:  57.27000045776367   kJ/mol  BindingDB
RITΔH:  3.759999990463257   kJ/mol  BindingDB
RIT-TΔS:  43.08000183105469   kJ/mol  BindingDB
RITΔH:  8.359999656677246   kJ/mol  BindingDB
RITΔG:  40.54999923706055   kJ/mol  BindingDB
RITΔH:  9.199999809265137   kJ/mol  BindingDB
RITΔH:  43.470001220703125   kJ/mol  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.414α = 90
b = 61.414β = 90
c = 80.816γ = 120
Software Package:
Software NamePurpose
CNSrefinement
SHELXrefinement
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-04-19
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2013-02-27
    Changes: Other