Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 22.34 kDa 
• Atom Count: 1669 
• Residue Count: 203 
• Unique protein chains: 2

1U8G

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

• DOI: 10.2210/pdb1U8G/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-08-06 Released: 2004-11-02 
• Deposition Author(s): Brynda, J., Rezacova, P., Fabry, M., Horejsi, M., Hradilek, M., Soucek, R., Stouracova, R., Konvalinka, J., Sedlacek, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.259 
• R-Value Work: 0.209 
• R-Value Observed: 0.211 

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 D Biol Crystallogr 60: 1943-1948

• PubMed: 15502300 
• DOI: 10.1107/S0907444904021572
• Primary Citation of Related Structures:  
  1U8G


• 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 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.

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Organizational Affiliation: 

Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16637 Praha 6, Czech Republic. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEASE RETROPEPSIN	A, B	99	Human immunodeficiency virus 1	Mutation(s): 0  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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
peptidomimetic inhibitor KI2-PHE-GLU-GLU-NH2	I	5	N/A	Mutation(s): 0

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000401	I	PEPTIDOMIMETIC INHIBITOR KI2-PHE-GLU-GLU-NH2	Peptide-like /  Inhibitor		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.259 
• R-Value Work: 0.209 
• R-Value Observed: 0.211 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.37	α = 90
b = 61.37	β = 90
c = 80.52	γ = 120

Software Package:

Software Name	Purpose
XDS	data scaling
XDS	data reduction
EPMR	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-08-06 
• Released Date: 2004-11-02 
Deposition Author(s): Brynda, J., Rezacova, P., Fabry, M., Horejsi, M., Hradilek, M., Soucek, R., Stouracova, R., Konvalinka, J., Sedlacek, J.

Revision History 

• Version 1.0: 2004-11-02
  Type: Initial release
  
• Version 1.1: 2008-04-30
  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: 2012-12-12
  Changes: Other
• Version 1.4: 2018-02-14
  Changes: Experimental preparation