8HVP

STRUCTURE AT 2.5-ANGSTROMS RESOLUTION OF CHEMICALLY SYNTHESIZED HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 PROTEASE COMPLEXED WITH A HYDROXYETHYLENE*-BASED INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structure at 2.5-A resolution of chemically synthesized human immunodeficiency virus type 1 protease complexed with a hydroxyethylene-based inhibitor.

Jaskolski, M.Tomasselli, A.G.Sawyer, T.K.Staples, D.G.Heinrikson, R.L.Schneider, J.Kent, S.B.Wlodawer, A.

(1991) Biochemistry 30: 1600-1609


  • PubMed Abstract: 
  • The crystal structure of a complex between chemically synthesized human immunodeficiency virus type 1 (HIV-1) protease and an octapeptide inhibitor has been refined to an R factor of 0.138 at 2.5-A resolution. The substrate-based inhibitor, H-Val-Ser ...

    The crystal structure of a complex between chemically synthesized human immunodeficiency virus type 1 (HIV-1) protease and an octapeptide inhibitor has been refined to an R factor of 0.138 at 2.5-A resolution. The substrate-based inhibitor, H-Val-Ser-Gln-Asn-Leu psi [CH(OH)CH2]Val-Ile-Val-OH (U-85548e) contains a hydroxyethylene isostere replacement at the scissile bond that is believed to mimic the tetrahedral transition state of the proteolytic reaction. This potent inhibitor has Ki less than 1 nM and was developed as an active-site titrant of the HIV-1 protease. The inhibitor binds in an extended conformation and is involved in beta-sheet interactions with the active-site floor and flaps of the enzyme, which form the substrate/inhibitor cavity. The inhibitor diastereomer has the S configuration at the chiral carbon atom of the hydroxyethylene insert, and the hydroxyl group is within H-bonding distance of the two active-site carboxyl groups in the enzyme dimer. The two subunits of the enzyme are related by a pseudodyad, which superposes them at a 178 degrees rotation. The main difference between the subunits is in the beta turns of the flaps, which have different conformations in the two monomers. The inhibitor has a clear preferred orientation in the active site and the alternative conformation, if any, is a minor one (occupancy of less than 30%). A new model of the enzymatic mechanism is proposed in which the proteolytic reaction is viewed as a one-step process during which the nucleophile (water molecule) and electrophile (an acidic proton) attack the scissile bond in a concerted manner.


    Related Citations: 
    • Enzymatic Activity of a Synthetic 99 Residue Protein Corresponding to the Putative HIV-1 Protease
      Schneider, J.,Kent, S.B.H.
      (1988) Cell 54: 363
    • Conserved Folding in Retroviral Proteases. Crystal Structure of a Synthetic HIV-1 Protease
      Wlodawer, A.,Miller, M.,Jaskolski, M.,Sathyanarayana, B.K.,Baldwin, E.,Weber, I.T.,Selk, L.M.,Clawson, L.,Schneider, J.,Kent, S.B.H.
      (1989) Science 245: 616
    • Molecular Modeling of the HIV-1 Protease and its Substrate Binding Site
      Weber, I.T.,Miller, M.,Jaskolski, M.,Leis, J.,Skalka, A.M.,Wlodawer, A.
      (1989) Science 243: 928
    • Crystal Structure of a Retroviral Protease Proves Relationship to Aspartic Protease Family
      Miller, M.,Jaskolski, M.,Rao, J.K.M.,Leis, J.,Wlodawer, A.
      (1989) Nature 337: 576


    Organizational Affiliation

    Macromolecular Structure Laboratory, National Cancer Institute-Frederick Cancer Research and Development Center, Maryland 21702-1201.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 PROTEASE
A, B
99Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2)Mutation(s): 0 
Gene Names: gag-pol
Find proteins for P03369 (Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2))
Go to UniProtKB:  P03369
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
INHIBITOR VAL-SER-GLN-ASN-LEU-PSI(CH(OH)-CH2)-VAL-ILE-VAL (U-85548E)
I
7N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000362
Query on PRD_000362
IINHIBITOR VAL-SER-GLN-ASN-LEU-PSI(CH(OH)-CH2)-VAL-ILE-VAL (U-85548E)Peptide-like / Inhibitor

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Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ABA
Query on ABA
A, B
L-PEPTIDE LINKINGC4 H9 N O2ALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.650α = 90.00
b = 58.760β = 90.00
c = 61.620γ = 90.00
Software Package:
Software NamePurpose
PROFFTrefinement

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: 2008-03-03
    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: 2012-12-12
    Type: Other
  • Version 1.4: 2017-11-29
    Type: Derived calculations, Other