2H4Y Hydrolase Hydrolase Inhibitor date May 25, 2006
title Crystal Structure Of Human Caspase-1 (Arg286->Lys) In Comple [2-(2-Benzyloxycarbonylamino-3-Methyl-Butyrylamino)-Propion 4-Oxo-Pentanoic Acid (Z-Vad-Fmk)
authors J.M.Scheer, J.A.Wells, M.J.Romanowski
compound source
Molecule: Caspase-1
Chain: A
Fragment: P20 Subunit, Residues 120-297
Ec: 3.4.22.36
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Casp1, Il1bc, Il1bce
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3) Codon+
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Prset

Molecule: Caspase-1
Chain: B
Fragment: P10 Subunit, Residues 317-404
Ec: 3.4.22.36
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Casp1, Il1bc, Il1bce
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3) Codon+
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Prset

Molecule: N-[(Benzyloxy)Carbonyl]-L-Valyl-N-[(2s)-1-Carboxy 3-Oxobutan-2-Yl]-L-Alaninamide;
Chain: C
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 43 21 2
R_factor 0.203 R_Free 0.235
crystal
cell
length a length b length c angle alpha angle beta angle gamma
63.343 63.343 141.607 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand CF0, PHQ enzyme Hydrolase E.C.3.4.22.36 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceAn allosteric circuit in caspase-1., Datta D, Scheer JM, Romanowski MJ, Wells JA, J Mol Biol. 2008 Sep 19;381(5):1157-67. Epub 2008 Jun 20. PMID:18590738
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (51 Kb) [Save to disk]
  • Biological Unit Coordinates (2h4y.pdb1.gz) 88 Kb
  • LPC: Ligand-Protein Contacts for 2H4Y
  • CSU: Contacts of Structural Units for 2H4Y
  • Likely Quarternary Molecular Structure file(s) for 2H4Y
  • Structure Factors (154 Kb)
  • Retrieve 2H4Y in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2H4Y from S2C, [Save to disk]
  • Re-refined 2h4y structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2H4Y 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 2H4Y
  • 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 2H4Y, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2h4y_B] [2h4y_A] [2h4y] [2h4y_C]
  • SWISS-PROT database: [P29466]
  • Domain organization of [CASP1_HUMAN] by SWISSPFAM
  • Domain found in 2H4Y: [CASc ] by SMART
  • Other resources with information on 2H4Y
  • Community annotation for 2H4Y 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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