3TOG

HIV-1 Protease - Epoxydic Inhibitor Complex (pH 9 - Monoclinic Crystal form P21)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.24 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Triggering reactions in crystals of HIV-1 protease complexes at varied pH

Geremia, S.Olajuyigbe, F.M.Ajele, J.O.Demitri, N.Randaccio, L.Wuerges, J.Benedetti, L.Campaner, P.Berti, F.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Gag-Pol polyprotein
A, B, C, D
99Human immunodeficiency virus type 1 group M subtype BMutation(s): 5 
Gene Names: gag-pol
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P03367
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DMS
Query on DMS

Download SDF File 
Download CCD File 
A, B, D
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
079
Query on 079

Download SDF File 
Download CCD File 
A, D
(S)-N-((2S,3S,4R,5R)-4-amino-3,5-dihydroxy-1,6-diphenylhexan-2-yl)-3-methyl-2-(2-phenoxyacetamido)butanamide
C31 H39 N3 O5
ASWZRLFSSZUWDR-UZMSACSVSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001019 (079)
Query on PRD_001019
A,D(S)-N-((2S,3S,4R,5R)-4-AMINO-3,5-DIHYDROXY-1,6-DIPHENYLHEXAN-2-YL)-3-METHYL-2-(2-PHENOXYACETAMIDO)BUTANAMIDEPeptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.24 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.242 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 51.191α = 90.00
b = 62.136β = 98.73
c = 58.751γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
HKL-2000data collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-15
    Type: Initial release
  • Version 1.1: 2012-12-12
    Type: Other
  • Version 1.2: 2014-10-29
    Type: Structure summary
  • Version 1.3: 2017-11-08
    Type: Refinement description