2C2K Hydrolase Hydrolase Inhibitor date Sep 29, 2005
title Crystal Structures Of Caspase-3 In Complex With Aza-Peptide Acceptor Inhibitors.
authors R.Ganesan, S.Jelakovic, O.D.Ekici, Z.Z.Li, K.E.James, J.L.Asgian, A.J.Campbell, J.Mikolajczyk, G.S.Salvesen, M.G.Gruetter, J.C.Po
compound source
Molecule: Caspase-3 Subunit P17
Chain: A
Fragment: Alpha Subunit, Residues 29-175
Ec: 3.4.22.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_vector: Pet11d

Molecule: Caspase-3 Subunit P12
Chain: B
Fragment: Beta Subunit, Residues 176-277
Ec: 3.4.22.-
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Aza-Peptide Inhibitor (5s, 8r, 11s)-8-(2-Carboxye (Carboxymethyl)-14-(4-Ethoxy-4-Oxobutanoyl)-11-(1-Methyleth 12-Tetraoxo-1-Phenyl-2-Oxa-4,7,10,13,14-Pentaazahexadecan - Acid;
Chain: C
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: I 2 2 2
R_factor 0.185 R_Free 0.220
crystal
cell
length a length b length c angle alpha angle beta angle gamma
67.471 83.781 96.251 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.87 Å
ligand AA1, PHQ enzyme Hydrolase E.C.3.4.22 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceDesign, synthesis, and evaluation of aza-peptide Michael acceptors as selective and potent inhibitors of caspases-2, -3, -6, -7, -8, -9, and -10., Ekici OD, Li ZZ, Campbell AJ, James KE, Asgian JL, Mikolajczyk J, Salvesen GS, Ganesan R, Jelakovic S, Grutter MG, Powers JC, J Med Chem. 2006 Sep 21;49(19):5728-49. PMID:16970398
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (54 Kb) [Save to disk]
  • Biological Unit Coordinates (2c2k.pdb1.gz) 95 Kb
  • LPC: Ligand-Protein Contacts for 2C2K
  • CSU: Contacts of Structural Units for 2C2K
  • Likely Quarternary Molecular Structure file(s) for 2C2K
  • Structure Factors (178 Kb)
  • Retrieve 2C2K in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2C2K from S2C, [Save to disk]
  • Re-refined 2c2k structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2C2K in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 2C2K
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2C2K, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2c2k_C] [2c2k_I] [2c2k] [2c2k_B] [2c2k_A]
  • SWISS-PROT database: [P42574]
  • Domain organization of [CASP3_HUMAN] by SWISSPFAM
  • Domain found in 2C2K: [CASc ] by SMART
  • Other resources with information on 2C2K
  • Community annotation for 2C2K at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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