1U8G

Crystal structure of a HIV-1 Protease in complex with peptidomimetic inhibitor KI2-PHE-GLU-GLU-NH2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.201 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Inhibitor binding at the protein interface in crystals of a HIV-1 protease complex.

Brynda, J.Rezacova, P.Fabry, M.Horejsi, M.Stouracova, R.Soucek, M.Hradilek, M.Konvalinka, J.Sedlacek, J.

(2004) Acta Crystallogr.,Sect.D 60: 1943-1948

  • DOI: 10.1107/S0907444904021572

  • PubMed Abstract: 
  • Depending on the excess of ligand used for complex formation, the HIV-1 protease complexed with a novel phenylnorstatine inhibitor forms crystals of either hexagonal (P6(1)) or orthorhombic (P2(1)2(1)2(1)) symmetry. The orthorhombic form shows an unu ...

    Depending on the excess of ligand used for complex formation, the HIV-1 protease complexed with a novel phenylnorstatine inhibitor forms crystals of either hexagonal (P6(1)) or orthorhombic (P2(1)2(1)2(1)) symmetry. The orthorhombic form shows an unusual complexity of crystal packing: in addition to one inhibitor molecule that is bound to the enzyme active site, the second inhibitor molecule is bound as an outer ligand at the protein interface. Binding of the outer ligand apparently increases the crystal-quality parameters so that the diffraction data allow solution of the structure of the complex at 1.03 A, the best resolution reported to date. The outer ligand interacts with all four surrounding HIV-1 protease molecules and has a bent conformation owing to its accommodation in the intermolecular space. The parameters of the solved structures of the orthorhombic and hexagonal forms are compared.


    Organizational Affiliation

    Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16637 Praha 6, Czech Republic. brynda@img.cas.cz




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEASE RETROPEPSIN
A, B
99Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI)Mutation(s): 0 
Gene Names: gag-pol
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI))
Go to UniProtKB:  P03367
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
peptidomimetic inhibitor KI2-PHE-GLU-GLU-NH2
I
5N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000401
Query on PRD_000401
IPEPTIDOMIMETIC INHIBITOR KI2-PHE-GLU-GLU-NH2Peptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.201 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.209 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 61.370α = 90.00
b = 61.370β = 90.00
c = 80.520γ = 120.00
Software Package:
Software NamePurpose
EPMRphasing
XDSdata reduction
REFMACrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-11-02
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Type: Other
  • Version 1.4: 2018-02-14
    Type: Experimental preparation