3YGS Apoptosis date May 08, 1999
title Apaf-1 Card In Complex With Prodomain Of Procaspase-9
authors H.Qin, S.Srinivasula, G.Wu, T.Fernandes-Alnemri, E.Alnemri, Y.Shi
compound source
Molecule: Apoptotic Protease Activating Factor 1
Chain: C
Fragment: Caspase Recruitment Domain (Card)
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cellular_location: Cytoplasm
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_plasmid: Pgex-2t

Molecule: Procaspase 9
Chain: P
Fragment: Prodomain
Ec: 3.4.22.-
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cellular_location: Cytoplasm
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_plasmid: Pgex-2t
symmetry Space Group: P 62 2 2
R_factor 0.224 R_Free 0.299
crystal
cell
length a length b length c angle alpha angle beta angle gamma
92.500 92.500 136.800 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.50 Å
ligand
enzyme Hydrolase E.C.3.4.22 BRENDA
note 3YGS is a representative structure
related structures by homologous chain: 1CWW, 1Z6T
Gene
Ontology
ChainFunctionProcessComponent
C


P


Primary referenceStructural basis of procaspase-9 recruitment by the apoptotic protease-activating factor 1., Qin H, Srinivasula SM, Wu G, Fernandes-Alnemri T, Alnemri ES, Shi Y, Nature 1999 Jun 10;399(6736):549-57. PMID:10376594
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (39 Kb) [Save to disk]
  • Biological Unit Coordinates (3ygs.pdb1.gz) 36 Kb
  • CSU: Contacts of Structural Units for 3YGS
  • Likely Quarternary Molecular Structure file(s) for 3YGS
  • Retrieve 3YGS in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3YGS from S2C, [Save to disk]
  • View 3YGS 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 3YGS
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3YGS, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d3ygsc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d3ygsp_, region P [Jmol] [rasmolscript] [script source]
  • Fold representative 3ygs 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: [3ygs_P] [3ygs_C] [3ygs]
  • SWISS-PROT database: [O14727] [P55211]
  • Domain organization of [APAF_HUMAN] [CASP9_HUMAN] by SWISSPFAM
  • Domain found in 3YGS: [CARD ] by SMART
  • Other resources with information on 3YGS
  • Community annotation for 3YGS at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Domain movements in 3YGS from the Database of Macromolecular Movements.
  • Images from IMB Jena Image Library of Biological Macromolecules.

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