2QAK

HIV-1 PR mutant in complex with nelfinavir


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Evolutionary pathway of HIV resistance analyzed on molecular level: Enzymatic activities, 3-D structures and thermodynamics of HIV proteases resistant to nelfinavir

Kozisek, M.Bray, J.Rezacova, P.Saskova, K.Rulisek, L.Brynda, J.Pokorna, J.Mammano, F.Konvalinka, J.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEASE RETROPEPSIN
A, B
99Human immunodeficiency virus 1Mutation(s): 3 
Gene Names: gag-pol
EC: 3.4.23.16
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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1UN
Query on 1UN

Download Ideal Coordinates CCD File 
C [auth A]2-[2-HYDROXY-3-(3-HYDROXY-2-METHYL-BENZOYLAMINO)-4-PHENYL SULFANYL-BUTYL]-DECAHYDRO-ISOQUINOLINE-3-CARBOXYLIC ACID TERT-BUTYLAMIDE
C32 H45 N3 O4 S
QAGYKUNXZHXKMR-HKWSIXNMSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
1UN BindingDB:  2QAK Ki: min: 0.07, max: 2 (nM) from 2 assay(s)
Kd: min: 3, max: 38 (nM) from 3 assay(s)
IC50: min: 1.9, max: 530 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.5α = 90
b = 62.5β = 90
c = 82.06γ = 120
Software Package:
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-08-30
    Changes: Data collection, Refinement description