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 

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Ligand Structure Quality Assessment 


This is version 1.4 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
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)
UniProt
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI))
Explore P03367 
Go to UniProtKB:  P03367
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03367
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RIT
Query on RIT

Download Ideal Coordinates CCD File 
C [auth A]RITONAVIR
C37 H48 N6 O5 S2
NCDNCNXCDXHOMX-XGKFQTDJSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
RIT BindingDB:  1RL8 Ki: min: 0.01, max: 109 (nM) from 36 assay(s)
Kd: min: 0.6, max: 0.61 (nM) from 2 assay(s)
IC50: min: 67, max: 9850 (nM) from 2 assay(s)
EC50: 150 (nM) from 1 assay(s)
-TΔS: min: -1.02e+2, max: -3.01e+1 (kJ/mol) from 42 assay(s)
ΔH: min: -2.76e+1, max: 73.15 (kJ/mol) from 44 assay(s)
ΔG: min: -6.02e+1, max: -2.88e+1 (kJ/mol) from 42 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001001 (RIT)
Query on PRD_001001
C [auth A]RITONAVIRPeptide-like / Inhibitor Ligand Interaction
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

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.4: 2021-10-27
    Changes: Data collection, Database references, Derived calculations