3EB6 Apoptosis, Ligase date Aug 27, 2008
title Structure Of The Ciap2 Ring Domain Bound To Ubch5b
authors P.D.Mace, K.Linke, F.R.Schumacher, C.A.Smith, C.L.Day
compound source
Molecule: Baculoviral Iap Repeat-Containing Protein 3
Chain: A
Fragment: Ring Domain (Residues 536 To 604)
Synonym: Inhibitor Of Apoptosis Protein 1, Hiap-1, Hiap1, C Tnfr2-Traf-Signaling Complex Protein 1, Iap Homolog C, Apop Inhibitor 2, Api2, Ring Finger Protein 49;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Birc3, Api2, Iap1, Mihc, Rnf49
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex6p3

Molecule: Ubiquitin-Conjugating Enzyme E2 D2
Chain: B
Synonym: Ubiquitin-Protein Ligase D2, Ubiquitin Carrier Pro Xubc4;
Ec: 6.3.2.19
Engineered: Yes

Organism_scientific: Xenopus Laevis
Organism_common: Clawed Frog, Platanna
Organism_taxid: 8355
Gene: Ube2d2, Ubc4
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex6p3
symmetry Space Group: P 63 2 2
R_factor 0.281 R_Free 0.320
crystal
cell
length a length b length c angle alpha angle beta angle gamma
137.226 137.226 111.870 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.40 Å
ligand ZN enzyme Ligase E.C.6.3.2.19 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
B


Primary referenceStructures of the cIAP2 RING Domain Reveal Conformational Changes Associated with Ubiquitin-conjugating Enzyme (E2) Recruitment., Mace PD, Linke K, Feltham R, Schumacher FR, Smith CA, Vaux DL, Silke J, Day CL, J Biol Chem. 2008 Nov 14;283(46):31633-40. Epub 2008 Sep 10. PMID:18784070
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (40 Kb) [Save to disk]
  • Biological Unit Coordinates (3eb6.pdb1.gz) 67 Kb
  • LPC: Ligand-Protein Contacts for 3EB6
  • CSU: Contacts of Structural Units for 3EB6
  • Likely Quarternary Molecular Structure file(s) for 3EB6
  • Structure Factors (134 Kb)
  • Retrieve 3EB6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3EB6 from S2C, [Save to disk]
  • Re-refined 3eb6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3EB6 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 3EB6
  • 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 3EB6, from MSDmotif at EBI
  • Fold representative 3eb6 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3eb6_A] [3eb6_B] [3eb6]
  • SWISS-PROT database: [Q13489] [P62840]
  • Domain organization of [BIRC3_HUMAN] [UB2D2_XENLA] by SWISSPFAM
  • Domains found in 3EB6: [RING] [UBCc ] by SMART
  • Other resources with information on 3EB6
  • Community annotation for 3EB6 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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