1LB6 Signaling Protein date Apr 02, 2002
title Traf6-Cd40 Complex
authors H.Ye, J.R.Arron, B.Lamothe, M.Cirilli, T.Kobayashi, N.K.Shevde, D.Segal, O.Dzivenu, M.Vologodskaia, M.Yim, K.Du, S.Singh, J.W.Pike, B.G.Darnay, Y.Choi, H.Wu
compound source
Molecule: Tnf Receptor-Associated Factor 6
Chain: A
Fragment: Residues 347-504
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Traf6
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Cd40 Antigen
Chain: B
Fragment: Residues 230-238
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cd40
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.203 R_Free 0.258
crystal
cell
length a length b length c angle alpha angle beta angle gamma
39.879 43.815 101.435 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
related structures by homologous chain: 1LB4
Primary referenceDistinct molecular mechanism for initiating TRAF6 signalling., Ye H, Arron JR, Lamothe B, Cirilli M, Kobayashi T, Shevde NK, Segal D, Dzivenu OK, Vologodskaia M, Yim M, Du K, Singh S, Pike JW, Darnay BG, Choi Y, Wu H, Nature 2002 Jul 25;418(6896):443-7. PMID:12140561
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (33 Kb) [Save to disk]
  • Biological Unit Coordinates (1lb6.pdb1.gz) 30 Kb
  • CSU: Contacts of Structural Units for 1LB6
  • Likely Quarternary Molecular Structure file(s) for 1LB6
  • Retrieve 1LB6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1LB6 from S2C, [Save to disk]
  • View 1LB6 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 1LB6
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1LB6, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1lb6a_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1lb6 from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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: [1lb6_B] [1lb6_A] [1lb6]
  • SWISS-PROT database: [P25942] [Q9Y4K3]
  • Domain organization of [TNR5_HUMAN] [TRAF6_HUMAN] by SWISSPFAM
  • Domain found in 1LB6: [MATH ] by SMART
  • Alignments of the sequence of 1LB6 with the sequences similar proteins can be viewed for 1LB6's classification [TNR5_HUMAN] [TRAF6_HUMAN] 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 [TNR5_HUMAN] [TRAF6_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1LB6
  • Community annotation for 1LB6 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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