3IFD Cytokine date Jul 24, 2009
title Human Synthetic Monocyte Chemoattractant Protein 1 (Mcp-1)
authors A.Teplyakov, G.Obmolova, G.L.Gilliland
compound source
Molecule: C-C Motif Chemokine 2
Chain: A
Fragment: Residues 24-99
Synonym: Small-Inducible Cytokine A2, Monocyte Chemoattract Protein 1, Monocyte Chemotactic Protein 1, Mcp-1, Monocyte Chemotactic And Activating Factor, Mcaf, Monocyte Secretory Je, Hc11;
Engineered: Yes
Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 32 2 1
R_factor 0.193 R_Free 0.255
crystal
cell
length a length b length c angle alpha angle beta angle gamma
60.710 60.710 45.490 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.90 Å
ligand K, PO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceSynthesis by native chemical ligation and crystal structure of human CCL2., Grygiel TL, Teplyakov A, Obmolova G, Stowell N, Holland R, Nemeth JF, Pomerantz SC, Kruszynski M, Gilliland GL, Biopolymers. 2010;94(3):350-9. PMID:20091676
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (16 Kb) [Save to disk]
  • Biological Unit Coordinates (3ifd.pdb1.gz) 23 Kb
  • LPC: Ligand-Protein Contacts for 3IFD
  • CSU: Contacts of Structural Units for 3IFD
  • Structure Factors (42 Kb)
  • Retrieve 3IFD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3IFD from S2C, [Save to disk]
  • Re-refined 3ifd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3IFD 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 3IFD
  • 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 3IFD, from MSDmotif at EBI
  • Fold representative 3ifd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ifd_A] [3ifd]
  • SWISS-PROT database: [P13500]
  • Domain organization of [CCL2_HUMAN] by SWISSPFAM
  • Domain found in 3IFD: [SCY ] by SMART
  • Other resources with information on 3IFD
  • Community annotation for 3IFD 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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