3KA2

Crystal structure of chemically synthesized 203 amino acid 'covalent dimer' [L-Ala;Gly51']HIV-1 protease molecule complexed with MVT-101 reduced isostere inhibitor at 1.4 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Protein conformational dynamics in the mechanism of HIV-1 protease catalysis.

Torbeev, V.Y.Raghuraman, H.Hamelberg, D.Tonelli, M.Westler, W.M.Perozo, E.Kent, S.B.

(2011) Proc Natl Acad Sci U S A 108: 20982-20987

  • DOI: 10.1073/pnas.1111202108
  • Primary Citation of Related Structures:  
    3FSM, 3HAU, 3HAW, 3HBO, 3HDK, 3HLO, 3IAW, 3KA2, 3NWQ, 3NWX, 3NXE, 3NXN, 3NYG

  • PubMed Abstract: 
  • We have used chemical protein synthesis and advanced physical methods to probe dynamics-function correlations for the HIV-1 protease, an enzyme that has received considerable attention as a target for the treatment of AIDS. Chemical synthesis was used to prepare a series of unique analogues of the HIV-1 protease in which the flexibility of the "flap" structures (residues 37-61 in each monomer of the homodimeric protein molecule) was systematically varied ...

    We have used chemical protein synthesis and advanced physical methods to probe dynamics-function correlations for the HIV-1 protease, an enzyme that has received considerable attention as a target for the treatment of AIDS. Chemical synthesis was used to prepare a series of unique analogues of the HIV-1 protease in which the flexibility of the "flap" structures (residues 37-61 in each monomer of the homodimeric protein molecule) was systematically varied. These analogue enzymes were further studied by X-ray crystallography, NMR relaxation, and pulse-EPR methods, in conjunction with molecular dynamics simulations. We show that conformational isomerization in the flaps is correlated with structural reorganization of residues in the active site, and that it is preorganization of the active site that is a rate-limiting factor in catalysis.


    Organizational Affiliation

    Department of Chemistry, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
[L-Ala51;Gly51']HIV-1 proteaseA203N/AMutation(s): 0 
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2NC (Subject of Investigation/LOI)
Query on 2NC

Download Ideal Coordinates CCD File 
B [auth A]N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide
C35 H68 N11 O8
MQPXOVRKKPPKFZ-QYKDHROSSA-O
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
ABA
Query on ABA
AL-PEPTIDE LINKINGC4 H9 N O2ALA
NLE
Query on NLE
AL-PEPTIDE LINKINGC6 H13 N O2LEU
YCM
Query on YCM
AL-PEPTIDE LINKINGC5 H10 N2 O3 SCYS
Binding Affinity Annotations 
IDSourceBinding Affinity
2NC PDBBind:  3KA2 Kd: 240 (nM) from 1 assay(s)
Binding MOAD:  3KA2 Kd: 240 (nM) from 1 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.695α = 90
b = 58.074β = 90
c = 61.593γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-04-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-01-11
    Changes: Database references
  • Version 1.3: 2012-09-12
    Changes: Refinement description
  • Version 1.4: 2012-12-12
    Changes: Other