1SDV

Crystal structures of HIV protease V82A and L90M mutants reveal changes in indinavir binding site.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.160 

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This is version 1.2 of the entry. See complete history


Literature

Crystal structures of HIV protease V82A and L90M mutants reveal changes in the indinavir-binding site

Mahalingam, B.Wang, Y.-F.Boross, P.I.Tozser, J.Louis, J.M.Harrison, R.W.Weber, I.T.

(2004) Eur J Biochem 271: 1516-1524

  • DOI: 10.1111/j.1432-1033.2004.04060.x
  • Primary Citation of Related Structures:  
    1SDT, 1SDU, 1SDV

  • PubMed Abstract: 
  • The crystal structures of the wild-type HIV-1 protease (PR) and the two resistant variants, PR(V82A) and PR(L90M), have been determined in complex with the antiviral drug, indinavir, to gain insight into the molecular basis of drug resistance. V82A and L90M correspond to an active site mutation and nonactive site mutation, respectively ...

    The crystal structures of the wild-type HIV-1 protease (PR) and the two resistant variants, PR(V82A) and PR(L90M), have been determined in complex with the antiviral drug, indinavir, to gain insight into the molecular basis of drug resistance. V82A and L90M correspond to an active site mutation and nonactive site mutation, respectively. The inhibition (K(i)) of PR(V82A) and PR(L90M) was 3.3- and 0.16-fold, respectively, relative to the value for PR. They showed only a modest decrease, of 10-15%, in their k(cat)/K(m) values relative to PR. The crystal structures were refined to resolutions of 1.25-1.4 A to reveal critical features associated with inhibitor resistance. PR(V82A) showed local changes in residues 81-82 at the site of the mutation, while PR(L90M) showed local changes near Met90 and an additional interaction with indinavir. These structural differences concur with the kinetic data.


    Organizational Affiliation

    Department of Biology, Georgia State University, PO Box 4010, Atlanta, GA 30302-4010, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
protease RETROPEPSINA, B99Human immunodeficiency virus 1Mutation(s): 6 
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)
UniProt
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI))
Explore P03367 
Go to UniProtKB:  P03367
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MK1 (Subject of Investigation/LOI)
Query on MK1

Download Ideal Coordinates CCD File 
E [auth B]N-[2(R)-HYDROXY-1(S)-INDANYL]-5-[(2(S)-TERTIARY BUTYLAMINOCARBONYL)-4(3-PYRIDYLMETHYL)PIPERAZINO]-4(S)-HYDROXY-2(R)-PHENYLMETHYLPENTANAMIDE
C36 H47 N5 O4
CBVCZFGXHXORBI-PXQQMZJSSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
MK1 BindingDB:  1SDV Ki: min: 0.05, max: 398 (nM) from 49 assay(s)
Kd: min: 1.07, max: 5.5 (nM) from 4 assay(s)
IC50: min: 0.36, max: 370 (nM) from 22 assay(s)
-TΔS: min: -8.28e+1, max: -2.80e+1 (kJ/mol) from 38 assay(s)
ΔH: min: -3.34e+1, max: 51 (kJ/mol) from 38 assay(s)
ΔG: min: -6.31e+1, max: -3.18e+1 (kJ/mol) from 37 assay(s)
Binding MOAD:  1SDV Ki: 1.81 (nM) from 1 assay(s)
PDBBind:  1SDV Ki: 1.81 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.160 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.82α = 90
b = 58.726β = 90
c = 46.592γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-05-25
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance