2K01 Cytokine date Jan 23, 2008
title Structure Of A Locked Sdf1 Dimer
authors B.F.Volkman, C.T.Veldkamp, F.C.Peterson
compound source
Molecule: Stromal Cell-Derived Factor 1
Chain: A, C
Fragment: Sdf-1-Alpha(3-67) Domain
Synonym: Sdf-1, C-X-C Motif Chemokine 12, Pre-B Cell Growth Stimulating Factor, Pbsf, Hirh;
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cxcl12, Sdf1, Sdf1a, Sdf1b
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Sg130099[Prep4]
Expression_system_vector_type: Vector
Expression_system_vector: Pqe30-6ht
methodSolution NMR
A, C

Primary referenceStructural basis of CXCR4 sulfotyrosine recognition by the chemokine SDF-1/CXCL12., Veldkamp CT, Seibert C, Peterson FC, De la Cruz NB, Haugner JC 3rd, Basnet H, Sakmar TP, Volkman BF, Sci Signal. 2008 Sep 16;1(37):ra4. PMID:18799424
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (843 Kb) [Save to disk]
  • Biological Unit Coordinates (2k01.pdb1.gz) 43 Kb
  • CSU: Contacts of Structural Units for 2K01
  • Original NMR restraints for 2K01 from PDB
  • Retrieve 2K01 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2K01 from S2C, [Save to disk]
  • View 2K01 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 2K01
  • 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 2K01, from MSDmotif at EBI
  • Fold representative 2k01 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2k01_C] [2k01] [2k01_A]
  • SWISS-PROT database: [P48061]
  • Domain organization of [SDF1_HUMAN] by SWISSPFAM
  • Domain found in 2K01: [SCY ] by SMART
  • Other resources with information on 2K01
  • Community annotation for 2K01 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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