2HBQ Hydrolase Hydrolase Inhibitor date Jun 14, 2006
title Crystal Structure Of Wildtype Human Caspase-1 In Complex Wit Benzyloxycarbonylamino-3-Methyl-Butyrylamino)-Propionylamin 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
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 0.208 R_Free 0.236
crystal
cell
length a length b length c angle alpha angle beta angle gamma
63.301 63.301 161.681 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand CF0, PHQ enzyme Hydrolase E.C.3.4.22.36 BRENDA
note 2HBQ supersedes 2FQR
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceA common allosteric site and mechanism in caspases., Scheer JM, Romanowski MJ, Wells JA, Proc Natl Acad Sci U S A. 2006 May 16;103(20):7595-600. Epub 2006 May 8. PMID:16682620
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (53 Kb) [Save to disk]
  • Biological Unit Coordinates (2hbq.pdb1.gz) 91 Kb
  • LPC: Ligand-Protein Contacts for 2HBQ
  • CSU: Contacts of Structural Units for 2HBQ
  • Likely Quarternary Molecular Structure file(s) for 2HBQ
  • Structure Factors (224 Kb)
  • Retrieve 2HBQ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2HBQ from S2C, [Save to disk]
  • Re-refined 2hbq structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2HBQ 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 2HBQ
  • 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 2HBQ, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2hbq_C] [2hbq_A] [2hbq_B] [2hbq]
  • SWISS-PROT database: [P29466]
  • Domain organization of [CASP1_HUMAN] by SWISSPFAM
  • Domain found in 2HBQ: [CASc ] by SMART
  • Other resources with information on 2HBQ
  • Community annotation for 2HBQ 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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