2RA4 Cytokine date Sep 14, 2007
title Crystal Structure Of Human Monocyte Chemoattractant Protein 4ccl13)
authors J.Lubkowski, C.Barinka
compound source
Molecule: Small-Inducible Cytokine A13
Chain: A, B
Synonym: Ccl13, Monocyte Chemotactic Protein 4, Mcp-4, Mono Chemoattractant Protein 4, Ck-Beta-10, Ncc-1;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ccl13, Mcp4, Ncc1, Scya13
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Trxb
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-11d
symmetry Space Group: I 4
R_factor 0.180 R_Free 0.216
crystal
cell
length a length b length c angle alpha angle beta angle gamma
74.673 74.673 51.650 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.70 Å
ligand SO4, TFA enzyme
note 2RA4 is a representative structure
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructure of human monocyte chemoattractant protein 4 (MCP-4/CCL13)., Barinka C, Prahl A, Lubkowski J, Acta Crystallogr D Biol Crystallogr. 2008 Mar;64(Pt 3):273-8. Epub 2008, Feb 20. PMID:18323622
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (30 Kb) [Save to disk]
  • Biological Unit Coordinates (2ra4.pdb1.gz) 25 Kb
  • Biological Unit Coordinates (2ra4.pdb2.gz) 97 Kb
  • Biological Unit Coordinates (2ra4.pdb3.gz) 50 Kb
  • Biological Unit Coordinates (2ra4.pdb4.gz) 49 Kb
  • LPC: Ligand-Protein Contacts for 2RA4
  • CSU: Contacts of Structural Units for 2RA4
  • Likely Quarternary Molecular Structure file(s) for 2RA4
  • Structure Factors (90 Kb)
  • Retrieve 2RA4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2RA4 from S2C, [Save to disk]
  • Re-refined 2ra4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2RA4 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 2RA4
  • 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 2RA4, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1u2ra4, region A:482-560 [Jmol] [rasmolscript] [script source]
  • Fold representative 2ra4 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ra4] [2ra4_B] [2ra4_A]
  • SWISS-PROT database: [Q99616]
  • Domain organization of [CCL13_HUMAN] by SWISSPFAM
  • Domain found in 2RA4: [SCY ] by SMART
  • Alignments of the sequence of 2RA4 with the sequences similar proteins can be viewed for 2RA4's classification [CCL13_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [CCL13_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 2RA4
  • Community annotation for 2RA4 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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