3D9T Apoptosis date May 27, 2008
title Ciap1-Bir3 In Complex With N-Terminal Peptide From Caspase- (Atpfqe)
authors R.Kulathila, A.Price
compound source
Molecule: Baculoviral Iap Repeat-Containing Protein 2
Chain: A, B
Synonym: Inhibitor Of Apoptosis Protein 2, Hiap2, Hiap-2, C-Iap1, Tnfr2-Traf-Signaling Complex Protein 2, Iap Homolog B, Ring Finger Protein 48;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Birc2, Api1, Iap2, Mihb, Rnf48
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 De3
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pnat40

Molecule: Caspase-9
Chain: C, D
Synonym: Casp-9, Ice-Like Apoptotic Protease 6, Ice-Lap6, Apoptotic Protease Mch-6, Apoptotic Protease-Activating Factor 3, Apaf-3, Caspase-9 Subunit P35, Caspase-9 Subunit P10;
Engineered: Yes

Synthetic: Yes
Other_details: Peptide Synthesized Based On N-Terminal Fragment Of Caspase-9 (Atpfqe).
symmetry Space Group: P 21 21 21
R_factor 0.183 R_Free 0.205
length a length b length c angle alpha angle beta angle gamma
30.268 68.427 122.358 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.50 Å
ligand ZN enzyme Hydrolase E.C. BRENDA
note 3D9T is a representative structure
Primary referenceThe structure of the BIR3 domain of cIAP1 in complex with the N-terminal peptides of SMAC and caspase-9., Kulathila R, Vash B, Sage D, Cornell-Kennon S, Wright K, Koehn J, Stams T, Clark K, Price A, Acta Crystallogr D Biol Crystallogr. 2009 Jan;65(Pt 1):58-66. Epub 2008, Dec 18. PMID:19153467
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (43 Kb) [Save to disk]
  • Biological Unit Coordinates (3d9t.pdb1.gz) 19 Kb
  • Biological Unit Coordinates (3d9t.pdb2.gz) 21 Kb
  • LPC: Ligand-Protein Contacts for 3D9T
  • CSU: Contacts of Structural Units for 3D9T
  • Likely Quarternary Molecular Structure file(s) for 3D9T
  • Structure Factors (583 Kb)
  • Retrieve 3D9T in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3D9T from S2C, [Save to disk]
  • Re-refined 3d9t structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3D9T 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 3D9T
  • 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 3D9T, from MSDmotif at EBI
  • Fold representative 3d9t from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3d9t] [3d9t_D] [3d9t_B] [3d9t_C] [3d9t_A]
  • SWISS-PROT database: [Q13490] [P55211]
  • Domain organization of [BIRC2_HUMAN] [CASP9_HUMAN] by SWISSPFAM
  • Domain found in 3D9T: [BIR ] by SMART
  • Other resources with information on 3D9T
  • Community annotation for 3D9T 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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