2VM9 Cell Adhesion date Jan 24, 2008
title Native Structure Of The Recombinant Discoidin II Of Dictyostelium Discoideum At 1.75 Angstrom
authors K.S.Aragao, M.Satre, A.Imberty, A.Varrot
compound source
Molecule: Discoidin-2
Chain: A
Synonym: Discoidin II
Engineered: Yes
Organism_scientific: Dictyostelium Discoideum
Organism_common: Slime Mold
Organism_taxid: 366501
Strain: Ax2
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: Rosetta2 Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pproexhtb
symmetry Space Group: H 3 2
R_factor 0.150 R_Free 0.178
crystal
cell
length a length b length c angle alpha angle beta angle gamma
81.833 81.833 257.823 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.75 Å
ligand CA, CL, MPD, PO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructure determination of Discoidin II from Dictyostelium discoideum and carbohydrate binding properties of the lectin domain., Aragao KS, Satre M, Imberty A, Varrot A, Proteins. 2008 Oct;73(1):43-52. PMID:18384150
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (55 Kb) [Save to disk]
  • Biological Unit Coordinates (2vm9.pdb1.gz) 147 Kb
  • LPC: Ligand-Protein Contacts for 2VM9
  • CSU: Contacts of Structural Units for 2VM9
  • Likely Quarternary Molecular Structure file(s) for 2VM9
  • Structure Factors (890 Kb)
  • Retrieve 2VM9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VM9 from S2C, [Save to disk]
  • Re-refined 2vm9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2VM9 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 2VM9
  • 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 2VM9, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vm9] [2vm9_A]
  • SWISS-PROT database: [P42530]
  • Domain organization of [DIS2_DICDI] by SWISSPFAM
  • Domain found in 2VM9: [FA58C ] by SMART
  • Other resources with information on 2VM9
  • Community annotation for 2VM9 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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