1DY9

Inhibition of the Hepatitis C Virus NS3/4A Protease. The Crystal Structures of Two Protease-Inhibitor Complexes (inhibitor I)

Structural Biology Knowledgebase: 1DY9 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.275
  • R-Value Work: 0.213

Literature

Macromolecules
Sequence Display for 1DY9

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 43955.93

Macromolecule Entities
Molecule Chains Length Organism Details
PROTEASE/HELICASE NS3 (P70) A, B 187 Hepatitis c virus EC#: 3.4.22 IUBMB
Fragment: PROTEASE
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
NONSTRUCTURAL PROTEIN NS4A (P4) C, D 16 Hepatitis c virus Fragment: RESIDUES 956-967
Mutation: T220K, P235K
Gene Name(s):

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
2ZF
Query on 2ZF

N-(tert-butoxycarbonyl)-L-alpha-glutamyl- N-[(1R)-1-(carboxycarbonyl)-3,3-difluoropropyl]- L-leucinamide
C21 H33 F2 N3 O9
WXVMZATZAOHPFR-AVGNSLFASA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000426
Query on PRD_000426
A, B BOC-GLU-LEU-FKI, PEPTIDE INHIBITOR Peptide-like /
Inhibitor
Ligand Explorer Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.275
  • R-Value Work: 0.213
  • Space Group: P 61
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 94.35 α = 90.00
b = 94.35 β = 90.00
c = 82.37 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2000-01-31
  • Released Date: 2001-01-28
  • Deposition author(s): Di Marco, S., Rizzi, M., Volpari, C., Walsh, M., Narjes, F., Colarusso, S., De Francesco, R., Matassa, V.G., Sollazzo, M.

Revision History

  • 2012-12-12
    Type: Other | Details: Add PRD info
  • 2011-07-13
    Type: Version format compliance | Details: Compliance with PDBx exchange dictionary V4
  • 2011-07-13
    Type: Atom nomenclature | Details: Atom nomenclature
  • 2011-07-13
    Type: Binding sites and description | Details: Binding sites and description
  • 2011-07-13
    Type: Non-polymer description | Details: Non-polymer description
  • 2011-07-13
    Type: Function and keywords | Details: Function and keywords
  • 2011-07-13
    Type: Linkage | Details: Linkage
  • 2011-07-13
    Type: Sequence database correspondence | Details: Sequence database correspondence
  • 2011-07-13
    Type: Polymer description | Details: Changed inhibitor presentation or chemistry