3HP3 Cytokine date Jun 03, 2009
title Crystal Structure Of Cxcl12
authors J.W.Murphy, E.Lolis, Y.Xiong, H.Yuan, G.Crichlow
compound source
Molecule: Cxcl12 Protein
Chain: A, B, C, D, E, F, G, H, I, J
Fragment: Unp Residues 22-88
Synonym: Stromal Cell-Derived Factor 1a, Cdna Flj76575, Hig Similar To Homo Sapiens Chemokine (C-X-C Motif) Ligand 12 (Stromalcell-Derived Factor 1) (Cxcl12), Mrna, Chemokine (C Motif) Ligand 12 (Stromal Cell-Derived Factor 1), Isoform C
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cxcl12, Hcg_25667
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22b
symmetry Space Group: P 21 21 21
R_factor 0.228 R_Free 0.280
crystal
cell
length a length b length c angle alpha angle beta angle gamma
41.834 117.468 134.501 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand AU enzyme
Gene HCG
Gene
Ontology
ChainFunctionProcessComponent
F, A, J, E, B, H, C, D, I, G


Primary referenceHeterologous quaternary structure of CXCL12 and its relationship to the CC chemokine family., Murphy JW, Yuan H, Kong Y, Xiong Y, Lolis EJ, Proteins. 2009 Dec 1. PMID:20077567
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (116 Kb) [Save to disk]
  • Biological Unit Coordinates (3hp3.pdb1.gz) 23 Kb
  • Biological Unit Coordinates (3hp3.pdb2.gz) 22 Kb
  • Biological Unit Coordinates (3hp3.pdb3.gz) 24 Kb
  • Biological Unit Coordinates (3hp3.pdb4.gz) 24 Kb
  • Biological Unit Coordinates (3hp3.pdb5.gz) 22 Kb
  • LPC: Ligand-Protein Contacts for 3HP3
  • CSU: Contacts of Structural Units for 3HP3
  • Structure Factors (413 Kb)
  • Retrieve 3HP3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3HP3 from S2C, [Save to disk]
  • Re-refined 3hp3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3HP3 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 3HP3
  • 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
  • 3D motif for 3HP3, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3hp3_F] [3hp3_C] [3hp3_B] [3hp3_I] [3hp3_G] [3hp3_H] [3hp3_A] [3hp3] [3hp3_J] [3hp3_E] [3hp3_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3HP3: [SCY ] by SMART
  • Other resources with information on 3HP3
  • Community annotation for 3HP3 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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