1PYO Hydrolase Hydrolase Inhibitor date Jul 09, 2003
title Crystal Structure Of Human Caspase-2 In Complex With Acetyl- Glu-Ser-Asp-Cho
authors A.Schweizer, C.Briand, M.G.Grutter
compound source
Molecule: Caspase-2
Chain: A, C
Fragment: Subunit P18, Sequence Database Residues 151-316
Synonym: Casp-2, Ich-1 Protease, Ich- 1l1s
Ec: 3.4.22.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Casp2 Or Ich1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21-Codonplus(De3)-Ril (Stratage
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet11d

Molecule: Caspase-2
Chain: B, D
Fragment: Subunit P12, Sequence Database Residues 331-435
Synonym: Casp-2, Ich-1 Protease, Ich- 1l1s
Ec: 3.4.22.-
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Casp2 Or Ich1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21-Codonplus(De3)-Ril (Stratage
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet11d

Molecule: Acetyl-Leu-Asp-Glu-Ser-Asj
Chain: E, F
Engineered: Yes

Synthetic: Yes
Organism_scientific: Saccharomyces Cerevisiae (Baker'S Yeas
Organism_taxid: 559292
Other_details: Synthetic, From Calbiochem
symmetry Space Group: P 21 21 21
R_factor 0.189 R_Free 0.213
crystal
cell
length a length b length c angle alpha angle beta angle gamma
63.649 96.583 97.547 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.65 Å
ligand ACE, ASJ enzyme Hydrolase E.C.3.4.22 BRENDA
note 1PYO is a representative structure
Gene
Ontology
ChainFunctionProcessComponent
A, C


D, B


Primary referenceCrystal structure of caspase-2, apical initiator of the intrinsic apoptotic pathway., Schweizer A, Briand C, Grutter MG, J Biol Chem 2003 Oct 24;278(43):42441-7. Epub 2003 Aug 14. PMID:12920126
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (98 Kb) [Save to disk]
  • Biological Unit Coordinates (1pyo.pdb1.gz) 94 Kb
  • LPC: Ligand-Protein Contacts for 1PYO
  • CSU: Contacts of Structural Units for 1PYO
  • Likely Quarternary Molecular Structure file(s) for 1PYO
  • Structure Factors (536 Kb)
  • Retrieve 1PYO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1PYO from S2C, [Save to disk]
  • Re-refined 1pyo structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1PYO 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 1PYO
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1PYO, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1pyo.1, region A:,B [Jmol] [rasmolscript] [script source]
        - Domain d1pyo.2, region C:,D [Jmol] [rasmolscript] [script source]
  • Fold representative 1pyo from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1pyo] [1pyo_A] [1pyo_D] [1pyo_E] [1pyo_C] [1pyo_F] [1pyo_B]
  • SWISS-PROT database: [P42575] [P36114]
  • Domain organization of [CASP2_HUMAN] [YKR18_YEAST] by SWISSPFAM
  • Domain found in 1PYO: [CASc ] by SMART
  • Other resources with information on 1PYO
  • Community annotation for 1PYO 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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