1QDU Hydrolase Hydrolase Inhibitor date Jul 10, 1999
title Crystal Structure Of The Complex Of Caspase-8 With The Tripe Ketone Inhibitor Zevd-Dcbmk
authors H.Blanchard, M.G.Grutter
compound source
Molecule: Caspase-8 Alpha-Chain
Chain: A, C, E, G, I, K
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_plasmid: Pet21b

Molecule: Caspase-8 Beta-Chain
Chain: B, D, F, H, J, L
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_plasmid: Pet21b

Molecule: Phq-Glu-Val-Asp-Dichloromethylketone Inhibitor
Chain: T, U, V, W, X, Y
Synonym: Z-Evd-Dcbmk
Engineered: Yes

Synthetic: Yes
Other_details: The Peptide Was Chemically Synthesized.
symmetry Space Group: C 1 2 1
R_factor 0.230 R_Free 0.302
crystal
cell
length a length b length c angle alpha angle beta angle gamma
93.900 206.530 102.050 90.00 102.30 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand 0QE, PHQ enzyme Hydrolase E.C.3.4.22 BRENDA
related structures by homologous chain: 1F9E, 1QTN
Gene
Ontology
ChainFunctionProcessComponent
A, K, E, C, I, G


F, J, B, H, D, L


Primary referenceThe three-dimensional structure of caspase-8: an initiator enzyme in apoptosis., Blanchard H, Kodandapani L, Mittl PR, Marco SD, Krebs JF, Wu JC, Tomaselli KJ, Grutter MG, Structure Fold Des 1999 Sep 15;7(9):1125-33. PMID:10508784
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (226 Kb) [Save to disk]
  • Biological Unit Coordinates (1qdu.pdb1.gz) 77 Kb
  • Biological Unit Coordinates (1qdu.pdb2.gz) 76 Kb
  • Biological Unit Coordinates (1qdu.pdb3.gz) 76 Kb
  • LPC: Ligand-Protein Contacts for 1QDU
  • CSU: Contacts of Structural Units for 1QDU
  • Likely Quarternary Molecular Structure file(s) for 1QDU
  • Structure Factors (371 Kb)
  • Retrieve 1QDU in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1QDU from S2C, [Save to disk]
  • Re-refined 1qdu structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1QDU 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 1QDU
  • 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 1QDU, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1qdu.1, region A:,B [Jmol] [rasmolscript] [script source]
        - Domain d1qdu.2, region C:,D [Jmol] [rasmolscript] [script source]
        - Domain d1qdu.3, region E:,F [Jmol] [rasmolscript] [script source]
        - Domain d1qdu.4, region G:,H [Jmol] [rasmolscript] [script source]
        - Domain d1qdu.5, region I:,J [Jmol] [rasmolscript] [script source]
        - Domain d1qdu.6, region K:,L [Jmol] [rasmolscript] [script source]
  • Fold representative 1qdu 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: [1qdu_Y] [1qdu_T] [1qdu_K] [1qdu_J] [1qdu_C] [1qdu_L] [1qdu_V] [1qdu_I] [1qdu_H] [1qdu] [1qdu_A] [1qdu_D] [1qdu_G] [1qdu_W] [1qdu_U] [1qdu_F] [1qdu_X] [1qdu_E] [1qdu_B]
  • SWISS-PROT database: [Q14790]
  • Domain organization of [CASP8_HUMAN] by SWISSPFAM
  • Domain found in 1QDU: [CASc ] by SMART
  • Other resources with information on 1QDU
  • Community annotation for 1QDU 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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