3HDK

Crystal structure of chemically synthesized [Aib51/51']HIV-1 protease

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

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This is version 1.3 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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
[Aib51/51']HIV-1 proteaseA, B99N/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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03369
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2NC
Query on 2NC
Download Ideal Coordinates CCD File 
C [auth B]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  4 Unique
IDChainsTypeFormula2D DiagramParent
ABA
Query on ABA		A, B L-PEPTIDE LINKINGC4 H9 N O2ALA
AIB
Query on AIB		A, B L-PEPTIDE LINKINGC4 H9 N O2ALA
NLE
Query on NLE		A, B L-PEPTIDE LINKINGC6 H13 N O2LEU
SMC
Query on SMC		A, B L-PEPTIDE LINKINGC4 H9 N O2 SCYS
Binding Affinity Annotations 
IDSourceBinding Affinity
2NC PDBBind:  3HDK Kd: 1.75e+4 (nM) from 1 assay(s)
Binding MOAD:  3HDK Kd: 1.75e+4 (nM) from 1 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.341α = 90
b = 58.395β = 90
c = 61.434γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2012-01-11
    Changes: Database references
  • Version 1.3: 2012-12-12
    Changes: Other