1A8K

CRYSTALLOGRAPHIC ANALYSIS OF HUMAN IMMUNODEFICIENCY VIRUS 1 PROTEASE WITH AN ANALOG OF THE CONSERVED CA-P2 SUBSTRATE: INTERACTIONS WITH FREQUENTLY OCCURRING GLUTAMIC ACID RESIDUE AT P2' POSITION OF SUBSTRATES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystallographic analysis of human immunodeficiency virus 1 protease with an analog of the conserved CA-p2 substrate -- interactions with frequently occurring glutamic acid residue at P2' position of substrates.

Weber, I.T.Wu, J.Adomat, J.Harrison, R.W.Kimmel, A.R.Wondrak, E.M.Louis, J.M.

(1997) Eur.J.Biochem. 249: 523-530


  • PubMed Abstract: 
  • Human immunodeficiency virus type 1 (HIV-1) protease hydrolysis of the Gag CA-p2 cleavage site is crucial for virion maturation and is optimal at acidic pH. To understand the processing of the CA-p2 site, we have determined the structure of HIV-1 pro ...

    Human immunodeficiency virus type 1 (HIV-1) protease hydrolysis of the Gag CA-p2 cleavage site is crucial for virion maturation and is optimal at acidic pH. To understand the processing of the CA-p2 site, we have determined the structure of HIV-1 protease complexed with an analog of the CA-p2 site, the reduced peptide inhibitor Arg-Val-Leu-r-Phe-Glu-Ala-Ahx-NH2 [r denotes the reduced peptide bond and Ahx 2-aminohexanoic acid (norleucine), respectively]. The crystal structure was refined to an R-factor of 0.17 at 0.21-nm resolution. The crystals have nearly the same lattice as related complexes in P2(1)2(1)2(1) which have twofold disordered inhibitor, but are in space group P2(1). and the asymmetric unit contains two dimers of HIV-1 protease related by 180 degrees rotation. An approximate non-crystallographic symmetry has replaced the exact crystal symmetry resulting in well-ordered inhibitor structure. Each protease dimer binds one ordered inhibitor molecule, but in opposite orientations. The interactions of the inhibitor with the two dimers are very similar for the central P2 Val to P2' Glu residues, but show more variation for the distal P3 Arg and P4' Ahx residues. Importantly, the carboxylate oxygens of Glu at P2' in the inhibitor are within hydrogen-bonding distance of a carboxylate oxygen of Asp30 of the protease suggesting that the two side chains share a proton. This interaction suggests that the enzyme-substrate complex is additionally stabilized at lower pH. The importance of this interaction is emphasized by the absence of polymorphisms of Asp30 in the protease and variants of P2' Glu in the critical CA-p2 cleavage site.


    Organizational Affiliation

    Department of Microbiology and Immunology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA. weber@asterix.jci.tju.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV PROTEASE
A, B, D, E
99Human immunodeficiency virus type 1 group M subtype BGene Names: gag-pol
EC: 3.4.23.16, 3.1.-.-, 2.7.7.49, 2.7.7.7, 3.1.26.13, 2.7.7.-, 3.1.13.2
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P03367
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0Q4
Query on 0Q4

Download SDF File 
Download CCD File 
A, E
N-[(2R)-2-({N~5~-[amino(iminio)methyl]-L-ornithyl-L-valyl}amino)-4-methylpentyl]-L-phenylalanyl-L-alpha-glutamyl-L-alanyl-L-norleucinamide
Inhibitor analogues of CA-p2
C40 H70 N11 O8
SGWAZUZKMXHYMB-UQGDEETHSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.174 
  • Space Group: P 1 1 21
Unit Cell:
Length (Å)Angle (°)
a = 59.600α = 90.00
b = 52.200β = 90.00
c = 61.700γ = 90.00
Software Package:
Software NamePurpose
R-AXISdata reduction
X-PLORmodel building
X-PLORphasing
X-PLORrefinement
R-AXISdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-01-13
    Type: Initial release
  • Version 1.1: 2008-03-24
    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