2MIP

CRYSTAL STRUCTURE OF HUMAN IMMUNODEFICIENCY VIRUS (HIV) TYPE 2 PROTEASE IN COMPLEX WITH A REDUCED AMIDE INHIBITOR AND COMPARISON WITH HIV-1 PROTEASE STRUCTURES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Crystal structure of human immunodeficiency virus (HIV) type 2 protease in complex with a reduced amide inhibitor and comparison with HIV-1 protease structures.

Tong, L.Pav, S.Pargellis, C.Do, F.Lamarre, D.Anderson, P.C.

(1993) Proc.Natl.Acad.Sci.USA 90: 8387-8391

  • DOI: 10.1073/pnas.90.18.8387

  • PubMed Abstract: 
  • The crystal structure of HIV-2 protease in complex with a reduced amide inhibitor [BI-LA-398; Phe-Val-Phe-psi (CH2NH)-Leu-Glu-Ile-amide] has been determined at 2.2-A resolution and refined to a crystallographic R factor of 17.6%. The rms deviation fr ...

    The crystal structure of HIV-2 protease in complex with a reduced amide inhibitor [BI-LA-398; Phe-Val-Phe-psi (CH2NH)-Leu-Glu-Ile-amide] has been determined at 2.2-A resolution and refined to a crystallographic R factor of 17.6%. The rms deviation from ideality in bond lengths is 0.018 A and in bond angles is 2.8 degrees. The largest structural differences between HIV-1 and HIV-2 proteases are located at residues 15-20, 34-40, and 65-73, away from the flap region and the substrate binding sites. The rms distance between equivalent C alpha atoms of HIV-1 and HIV-2 protease structures excluding these residues is 0.5 A. The shapes of the S1 and S2 pockets in the presence of this inhibitor are essentially unperturbed by the amino acid differences between HIV-1 and HIV-2 proteases. The interaction of the inhibitor with HIV-2 protease is similar to that observed in HIV-1 protease structures. The unprotected N terminus of the inhibitor interacts with the side chains of Asp-29 and Asp-30. The glutamate side chain of the inhibitor forms hydrogen bonds with the main-chain amido groups of residues 129 and 130.


    Organizational Affiliation

    Department of Medicinal Chemistry, Boehringer Ingelheim Pharmaceutical, Inc., Ridgefield, CT 06877.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-2 PROTEASE
A, B, C, D
99Human immunodeficiency virus type 2 subtype A (isolate ROD)Mutation(s): 0 
Gene Names: gag-pol
Find proteins for P04584 (Human immunodeficiency virus type 2 subtype A (isolate ROD))
Go to UniProtKB:  P04584
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
INHIBITOR BI-LA-398
E, F, G, H
7N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
E, F, G, H
NON-POLYMERH2 N

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Work: 0.176 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 55.100α = 90.00
b = 55.100β = 90.00
c = 138.900γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORphasing
TNTrefinement
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-10-31
    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: 2019-07-17
    Type: Data collection, Derived calculations, Other, Refinement description
  • Version 1.4: 2019-08-14
    Type: Data collection, Refinement description