3M0D Signaling Protein date Mar 02, 2010
title Crystal Structure Of The Traf1:Traf2:Ciap2 Complex
authors V.Kabaleeswaran, H.Wu
compound source
Molecule: Tnf Receptor-Associated Factor 2
Chain: A, B
Fragment: Residues 266-329
Synonym: Tumor Necrosis Factor Type 2 Receptor-Associated P
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Traf2
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)Ripl
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet26b

Molecule: Tnf Receptor-Associated Factor 1
Chain: C
Fragment: Residues 266-329
Synonym: Epstein-Barr Virus-Induced Protein 6
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Traf1, Ebi6
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Baculoviral Iap Repeat-Containing Protein 3
Chain: D
Fragment: Residues 26-99
Synonym: Inhibitor Of Apoptosis Protein 1, Iap-1, Hiap-1, H Iap2, Tnfr2-Traf-Signaling Complex Protein 1, Iap Homolog C Apoptosis 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
symmetry Space Group: I 41
R_factor 0.197 R_Free 0.247
length a length b length c angle alpha angle beta angle gamma
91.867 91.867 88.702 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand ZN enzyme
A, B


Primary referenceCrystal structures of the TRAF2: cIAP2 and the TRAF1: TRAF2: cIAP2 complexes: affinity, specificity, and regulation., Zheng C, Kabaleeswaran V, Wang Y, Cheng G, Wu H, Mol Cell. 2010 Apr 9;38(1):101-13. PMID:20385093
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (93 Kb) [Save to disk]
  • Biological Unit Coordinates (3m0d.pdb1.gz) 88 Kb
  • Biological Unit Coordinates (3m0d.pdb2.gz) 88 Kb
  • LPC: Ligand-Protein Contacts for 3M0D
  • CSU: Contacts of Structural Units for 3M0D
  • Structure Factors (80 Kb)
  • Retrieve 3M0D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3M0D from S2C, [Save to disk]
  • Re-refined 3m0d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3M0D 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 3M0D
  • 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 3M0D, from MSDmotif at EBI
  • Fold representative 3m0d from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3m0d_C] [3m0d] [3m0d_B] [3m0d_D] [3m0d_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3M0D: [BIR ] by SMART
  • Other resources with information on 3M0D
  • Community annotation for 3M0D 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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