5DNF Cytokine date Sep 10, 2015
title Crystal Structure Of Cc Chemokine 5 (Ccl5) Oligomer In Compl Heparin
authors W.G.Liang, W.Tang
compound source
Molecule: C-C Motif Chemokine 5
Chain: A, B, C, D, E, F, G, H, I
Fragment: Unp Residues 27-91
Synonym: Eocp,Eosinophil Chemotactic Cytokine,Sis-Delta,Sma Inducible Cytokine A5,T Cell-Specific Protein P228,Tcp228,T Specific Protein Rantes;
Engineered: Yes
Mutation: Yes
Other_details: Serine At The N-Terminal Has O-Linked Glycos Glucose.
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ccl5, D17s136e, Scya5
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 2 2 2
R_factor 0.181 R_Free 0.234
crystal
cell
length a length b length c angle alpha angle beta angle gamma
121.190 210.063 123.827 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.55 Å
ligand BGC, CL, GLA, IDS, SGN, SO4, TRS enzyme
Gene
Ontology
ChainFunctionProcessComponent
F, A, E, B, H, C, D, I, G
  • receptor signaling protein t...
  • CCR1 chemokine receptor bind...
  • chemoattractant activity
  • chemokine receptor antagonis...


  • Primary referenceStructural basis for oligomerization and glycosaminoglycan binding of CCL5 and CCL3., Liang WG, Triandafillou CG, Huang TY, Zulueta MM, Banerjee S, Dinner AR, Hung SC, Tang WJ, Proc Natl Acad Sci U S A. 2016 May 3;113(18):5000-5. doi:, 10.1073/pnas.1523981113. Epub 2016 Apr 18. PMID:27091995
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (114 Kb) [Save to disk]
  • Biological Unit Coordinates (5dnf.pdb1.gz) 107 Kb
  • LPC: Ligand-Protein Contacts for 5DNF
  • CSU: Contacts of Structural Units for 5DNF
  • Structure Factors (681 Kb)
  • Retrieve 5DNF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5DNF from S2C, [Save to disk]
  • Re-refined 5dnf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5DNF 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 5DNF
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5dnf_D] [5dnf_F] [5dnf_E] [5dnf_B] [5dnf_I] [5dnf_H] [5dnf] [5dnf_G] [5dnf_C] [5dnf_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5DNF: [SCY ] by SMART
  • Other resources with information on 5DNF
  • Community annotation for 5DNF at PDBWiki (http://pdbwiki.org)

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