4HVP

Structure of complex of synthetic HIV-1 protease with a substrate-based inhibitor at 2.3 Angstroms resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Structure of complex of synthetic HIV-1 protease with a substrate-based inhibitor at 2.3 A resolution.

Miller, M.Schneider, J.Sathyanarayana, B.K.Toth, M.V.Marshall, G.R.Clawson, L.Selk, L.Kent, S.B.Wlodawer, A.

(1989) Science 246: 1149-1152


  • PubMed Abstract: 
  • The structure of a complex between a peptide inhibitor with the sequence N-acetyl-Thr-Ile-Nle-psi[CH2-NH]-Nle-Gln-Arg.amide (Nle, norleucine) with chemically synthesized HIV-1 (human immunodeficiency virus 1) protease was determined at 2.3 A resoluti ...

    The structure of a complex between a peptide inhibitor with the sequence N-acetyl-Thr-Ile-Nle-psi[CH2-NH]-Nle-Gln-Arg.amide (Nle, norleucine) with chemically synthesized HIV-1 (human immunodeficiency virus 1) protease was determined at 2.3 A resolution (R factor of 0.176). Despite the symmetric nature of the unliganded enzyme, the asymmetric inhibitor lies in a single orientation and makes extensive interactions at the interface between the two subunits of the homodimeric protein. Compared with the unliganded enzyme, the protein molecule underwent substantial changes, particularly in an extended region corresponding to the "flaps" (residues 35 to 57 in each chain), where backbone movements as large as 7 A are observed.


    Related Citations: 
    • 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
    • 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
    • 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
    • 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


    Organizational Affiliation

    NCI-Frederick Cancer Research Facility, BRI-Basic Research Program, MD 21701.




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
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2NC
Query on 2NC

Download SDF File 
Download CCD File 
B
N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide
p2/NC
C35 H68 N11 O8
MQPXOVRKKPPKFZ-QYKDHROSSA-O
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ABA
Query on ABA
A, B
L-PEPTIDE LINKINGC4 H9 N O2ALA
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2NCKi: 780 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.700α = 90.00
b = 59.200β = 90.00
c = 62.450γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1990-04-15
    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: 2013-02-27
    Type: Other
  • Version 1.4: 2013-04-03
    Type: Structure summary
  • Version 1.5: 2017-11-29
    Type: Derived calculations, Other