1MTB

Viability of a drug-resistant HIV-1 protease mutant: structural insights for better antiviral therapy


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

Viability of drug-resistant human immunodeficiency virus type 1 protease variant: structural insights for better antiviral therapy

Prabu-Jeyabalan, M.Nalivaika, E.A.King, N.M.Schiffer, C.A.

(2003) J Virol 77: 1305-1315

  • DOI: https://doi.org/10.1128/jvi.77.2.1306-1315.2003
  • Primary Citation of Related Structures:  
    1MT7, 1MT8, 1MT9, 1MTB, 1N49

  • PubMed Abstract: 

    Under the selective pressure of protease inhibitor therapy, patients infected with human immunodeficiency virus (HIV) often develop drug-resistant HIV strains. One of the first drug-resistant mutations to arise in the protease, particularly in patients receiving indinavir or ritonavir treatment, is V82A, which compromises the binding of these and other inhibitors but allows the virus to remain viable. To probe this drug resistance, we solved the crystal structures of three natural substrates and two commercial drugs in complex with an inactive drug-resistant mutant (D25N/V82A) HIV-1 protease. Through structural analysis and comparison of the protein-ligand interactions, we found that Val82 interacts more closely with the drugs than with the natural substrate peptides. The V82A mutation compromises these interactions with the drugs while not greatly affecting the substrate interactions, which is consistent with previously published kinetic data. Coupled with our earlier observations, these findings suggest that future inhibitor design may reduce the probability of the appearance of drug-resistant mutations by targeting residues that are essential for substrate recognition.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester 01605, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEASE RETROPEPSIN
A, B
99Human immunodeficiency virus 1Mutation(s): 1 
EC: 3.4.23.16
UniProt
Find proteins for P03369 (Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2))
Explore P03369 
Go to UniProtKB:  P03369
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03369
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DIQ
Query on DIQ

Download Ideal Coordinates CCD File 
F [auth B]2-METHYL-DECAHYDRO-ISOQUINOLINE-3-CARBOXYLIC ACID
C11 H19 N O2
YKQLYDHGCIEUMU-AEJSXWLSSA-N
QNC
Query on QNC

Download Ideal Coordinates CCD File 
C [auth A]quinoline-2-carboxylic acid
C10 H7 N O2
LOAUVZALPPNFOQ-UHFFFAOYSA-N
HPH
Query on HPH

Download Ideal Coordinates CCD File 
E [auth A](2S)-2-amino-3-phenylpropane-1,1-diol
C9 H13 N O2
IFTWVTAUEXLCHB-QMMMGPOBSA-N
ASN
Query on ASN

Download Ideal Coordinates CCD File 
D [auth A]ASPARAGINE
C4 H8 N2 O3
DCXYFEDJOCDNAF-REOHCLBHSA-N
NTB
Query on NTB

Download Ideal Coordinates CCD File 
G [auth B]TERTIARY-BUTYLAMINE
C4 H11 N
YBRBMKDOPFTVDT-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.439α = 90
b = 60.039β = 90
c = 62.021γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-01-07
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2021-10-27
    Changes: Database references, Derived calculations
  • Version 1.5: 2024-02-14
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.6: 2024-03-13
    Changes: Source and taxonomy, Structure summary