3QD6 Cytokine Cytokine Receptor date Jan 18, 2011
title Crystal Structure Of The Cd40 And Cd154 (Cd40l) Complex
authors J.O.Lee, Y.J.Kim, D.H.Song, H.M.Kim, B.S.Park
compound source
Molecule: Cd40 Ligand
Chain: A, B, C, D, E, F
Fragment: Secreted Form, Soluble Form
Synonym: Cd40-L
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cd154, Cd40l
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_cell_line: High Five
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pacgp67a

Molecule: Tumor Necrosis Factor Receptor Superfamily Member
Chain: R, S, T, U
Fragment: Extracellular Domain
Synonym: Cd40l Receptor
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cd40
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pvl1393
symmetry Space Group: P 65
R_factor 0.245 R_Free 0.298
crystal
cell
length a length b length c angle alpha angle beta angle gamma
133.212 133.212 211.151 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.50 Å
ligand NAG enzyme
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, E, B


Primary referenceCrystallographic and mutational analysis of the CD40-CD154 complex and its implications for receptor activation., An HJ, Kim YJ, Song DH, Park BS, Kim HM, Lee JD, Paik SG, Lee JO, Lee H, J Biol Chem. 2011 Apr 1;286(13):11226-35. Epub 2011 Feb 1. PMID:21285457
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (209 Kb) [Save to disk]
  • Biological Unit Coordinates (3qd6.pdb1.gz) 103 Kb
  • Biological Unit Coordinates (3qd6.pdb2.gz) 103 Kb
  • LPC: Ligand-Protein Contacts for 3QD6
  • CSU: Contacts of Structural Units for 3QD6
  • Structure Factors (222 Kb)
  • Retrieve 3QD6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3QD6 from S2C, [Save to disk]
  • Re-refined 3qd6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3QD6 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 3QD6
  • 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 3QD6, from MSDmotif at EBI
  • Fold representative 3qd6 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3qd6_E] [3qd6_T] [3qd6_U] [3qd6_A] [3qd6_B] [3qd6_D] [3qd6_S] [3qd6_F] [3qd6_C] [3qd6_R] [3qd6]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3QD6: [TNF] [TNFR ] by SMART
  • Other resources with information on 3QD6
  • Community annotation for 3QD6 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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