2DKO	Hydrolase Hydrolase Inhibitor	date	Apr 12, 2006
title	Extended Substrate Recognition In Caspase-3 Revealed By High Resolution X-Ray Structure Analysis
authors	P.R.E.Mittl, R.Ganesan, S.Jelakovic, M.G.Grutter
compound		source
Molecule: Caspase-3 Chain: A Fragment: Caspase-3 P17 Subunit, Residues 29-174 Ec: 3.4.22.- Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet11d
Molecule: Caspase-3 Chain: B Fragment: Caspase-3 P12 Subunit, Residues 175-277 Ec: 3.4.22.- Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet11d
Molecule: Phq-Asp-Glu-Val-Asp-Chloromethylketone Chain: I Synonym: Z-Devd-Cmk Engineered: Yes		Synthetic: Yes Other_details: Chemically Synthesized
symmetry	Space Group: I 2 2 2	R_factor R_Free
crystal cell	length a length b length c angle alpha angle beta angle gamma 67.650 83.890 96.160 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	1.06 Å
ligand	0QE	enzyme	Hydrolase E.C.3.4.22 BRENDA
note	2DKO is a representative structure
Gene Ontology	Chain Function Process Component A B
Primary reference	Extended Substrate Recognition in Caspase-3 Revealed by High Resolution X-ray Structure Analysis., Ganesan R, Mittl PR, Jelakovic S, Grutter MG, J Mol Biol. 2006 Jun 23;359(5):1378-88. Epub 2006 May 11. PMID:16787777

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (95 Kb) [Save to disk] Biological Unit Coordinates (2dko.pdb1.gz) 180 Kb LPC: Ligand-Protein Contacts for 2DKO CSU: Contacts of Structural Units for 2DKO Likely Quarternary Molecular Structure file(s) for 2DKO Structure Factors (847 Kb) Retrieve 2DKO in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2DKO from S2C, [Save to disk] Re-refined 2dko structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2DKO 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 2DKO

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 2DKO, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2dko_A] [2dko] [2dko_I] [2dko_B] SWISS-PROT database: [P42574] Domain organization of [CASP3_HUMAN] by SWISSPFAM Domain found in 2DKO: [CASc ] by SMART

Other resources with information on 2DKO

Community annotation for 2DKO 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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