3R6L Hydrolase Hydrolase Inhibitor date Mar 21, 2011
title Caspase-2 T380a Bound With Ac-Vdvad-Cho
authors Y.Tang, J.Wells, M.Arkin
compound source
Molecule: Caspase-2 Subunit P18
Chain: A, C
Ec: 3.4.22.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Casp2, Ich1, Nedd2
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Caspase-2 Subunit P12
Chain: B, D
Ec: 3.4.22.-
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Casp2, Ich1, Nedd2
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Peptide Inhibitor (Ace)Vdvad-Cho
Chain: F, E
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 21 21 21
R_factor 0.168 R_Free 0.194
crystal
cell
length a length b length c angle alpha angle beta angle gamma
62.912 97.063 98.257 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand ACE, ASA enzyme Hydrolase E.C.3.4.22 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C


D, B


Primary referenceStructural and enzymatic insights into caspase-2 protein substrate recognition and catalysis., Tang Y, Wells JA, Arkin MR, J Biol Chem. 2011 Sep 30;286(39):34147-54. Epub 2011 Aug 2. PMID:21828056
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (97 Kb) [Save to disk]
  • Biological Unit Coordinates (3r6l.pdb1.gz) 46 Kb
  • Biological Unit Coordinates (3r6l.pdb2.gz) 48 Kb
  • Biological Unit Coordinates (3r6l.pdb3.gz) 91 Kb
  • LPC: Ligand-Protein Contacts for 3R6L
  • CSU: Contacts of Structural Units for 3R6L
  • Structure Factors (700 Kb)
  • Retrieve 3R6L in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3R6L from S2C, [Save to disk]
  • Re-refined 3r6l structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3R6L 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 3R6L
  • 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 3R6L, from MSDmotif at EBI
  • Fold representative 3r6l from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3r6l_C] [3r6l_B] [3r6l_A] [3r6l_E] [3r6l_F] [3r6l_D] [3r6l]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3R6L: [CASc ] by SMART
  • Other resources with information on 3R6L
  • Community annotation for 3R6L at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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