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
crystal
cell
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
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
  • Alignments of the sequence of 3M0D with the sequences similar proteins can be viewed for 3M0D's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • 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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