2WPO

HCMV protease inhibitor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.332 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Conserved mode of peptidomimetic inhibition and substrate recognition of human cytomegalovirus protease.

Tong, L.Qian, C.Massariol, M.J.Deziel, R.Yoakim, C.Lagace, L.

(1998) Nat.Struct.Mol.Biol. 5: 819-826

  • DOI: 10.1038/1860

  • PubMed Abstract: 
  • Human cytomegalovirus (HCMV) protease belongs to a new class of serine proteases, with a unique polypeptide backbone fold. The crystal structure of the protease in complex with a peptidomimetic inhibitor (based on the natural substrates and covering ...

    Human cytomegalovirus (HCMV) protease belongs to a new class of serine proteases, with a unique polypeptide backbone fold. The crystal structure of the protease in complex with a peptidomimetic inhibitor (based on the natural substrates and covering the P4 to P1' positions) has been determined at 2.7 A resolution. The inhibitor is bound in an extended conformation, forming an anti-parallel beta-sheet with the protease. The P3 and P1 side chains are less accessible to solvent, whereas the P4 and P2 side chains are more exposed. The inhibitor binding mode shows significant similarity to those observed for peptidomimetic inhibitors or substrates of other classes of serine proteases (chymotrypsin and subtilisin). HCMV protease therefore represents example of convergent evolution. In addition, large conformational differences relative to the structure of the free enzyme are observed, which may be important for inhibitor binding.


    Related Citations: 
    • A New Serine-Protease Fold Revealed by the Crystal Structure of Human Cytomegalovirus Protease
      Tong, L.,Qian, C.,Massariol, M.J.,Bonneau, P.R.,Cordingley, M.G.,Lagace, L.
      (1996) Nature 383: 272


    Organizational Affiliation

    Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut 06877, USA. tong@como.bio.columbia.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HUMAN CYTOMEGALOVIRUS PROTEASE
A, B, C, D
256Human cytomegalovirus (strain AD169)Mutation(s): 3 
Gene Names: UL80 (APNG)
Find proteins for P16753 (Human cytomegalovirus (strain AD169))
Go to UniProtKB:  P16753
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
01E
Query on 01E

Download SDF File 
Download CCD File 
A, B, C, D
(2S)-2-(3,3-dimethylbutanoylamino)-N-[(2S)-1-[[(2S,3S)-3-hydroxy-4-[(4-iodophenyl)methylamino]-4-oxo-butan-2-yl]amino]-1,4-dioxo-4-pyrrol-1-yl-butan-2-yl]-3,3-dimethyl-butanamide
BILC 821
C31 H44 I N5 O6
DUBMDYQWHSIBPD-FBESYSLLSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000229 (01E)
Query on PRD_000229
A,B,C,DBILC 821Peptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.332 
  • R-Value Work: 0.226 
  • Space Group: P 21 2 21
Unit Cell:
Length (Å)Angle (°)
a = 107.800α = 90.00
b = 53.400β = 90.00
c = 212.400γ = 90.00
Software Package:
Software NamePurpose
REPLACEphasing
REPLACEmodel building
DENZOdata reduction
SCALEPACKdata scaling
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-08-04
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Source and taxonomy, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Type: Other