2C2Z

CRYSTAL STRUCTURE OF CASPASE-8 IN COMPLEX WITH AZA-PEPTIDE MICHAEL ACCEPTOR INHIBITOR

Structural Biology Knowledgebase: 2C2Z SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.187
  • R-Value Work: 0.171

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2C2Z

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 31220.12

Macromolecule Entities
Molecule Chains Length Organism Details
CASPASE-8 P18 SUBUNIT A 159 Homo sapiens EC#: 3.4.22.61 IUBMB
Fragment: ALPHA SUB-UNIT, RESIDUES 218-374
Gene Name(s): CASP8 Gene View MCH5
CASPASE-8 P10 SUBUNIT B 106 Homo sapiens EC#: 3.4.22.61 IUBMB
Fragment: BETA-SUBUNIT, RESIDUES 376-479
Gene Name(s): CASP8 Gene View MCH5
AZA-PEPTIDE INHIBITOR (5S, 8R, 11S)-8-(2-CARBOXYETHYL) -14-[4-(3,4-DIHYDROQUINOLIN-1(2H)-YL)-4-OXOBUTANOYL] -11-[(1R)-1-HYDROXYETHYL]-5-(2-METHYLPROPYL)-3,6,9,12-TETRAOXO -1-PHENYL-2-OXA-4,7,10,13,14-PENTAAZAHEXADECAN-16-OIC ACID C 5 synthetic

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
DTD
Query on DTD

B DITHIANE DIOL
C4 H8 O2 S2
YPGMOWHXEQDBBV-IMJSIDKUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000336 (MX5,PHQ,THR,GLU,LEU) C Cbz-Leu-Glu-Thr-AAsp-CHCH-CON-tetrahydroquinoline Peptide-like /
Inhibitor
Ligand Explorer Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.187
  • R-Value Work: 0.171
  • Space Group: P 31 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 62.52 α = 90.00
b = 62.52 β = 90.00
c = 129.94 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-10-02
  • Released Date: 2006-09-20
  • Deposition author(s): Ganesan, R., Jelakovic, S., Ekici, O.D., Li, Z.Z., James, K.E., Asgian, J.L., Campbell, A.J., Mikolajczyk, J., Salvesen, G.S., Powers, J.C., Gruetter, M.G.

Revision History

  • 2012-12-12
    Type: Other | Details: Add PRD info
  • 2011-07-20
    Type: Polymer description | Details: COMPND
  • 2011-07-20
    Type: Other | Details: REMARK 4
  • 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
  • 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