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 Diffraction	resolution	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	Chain Function Process Component C P
Primary reference	Structural 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) 35 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

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server 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] 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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