2VDL Re-refinement of Integrin AlphaIIbBeta3 Headpiece date
authors Springer, T.A., Zhu, J., Xiao, T.
compound source
symmetry
R_factor
R_Free 0.191
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.75
ligand CA, CAC, GOL, MAN, MG, NAG enzyme
note 2VDL supersedes 1TXV
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceStructural basis for distinctive recognition of fibrinogen gammaC peptide by the platelet integrin alphaIIbbeta3., Springer TA, Zhu J, Xiao T, J Cell Biol. 2008 Aug 25;182(4):791-800. Epub 2008 Aug 18. PMID:18710925
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (250 Kb) [Save to disk]
  • Biological Unit Coordinates (2vdl.pdb1.gz) 236 Kb
  • LPC: Ligand-Protein Contacts for 2VDL
  • CSU: Contacts of Structural Units for 2VDL
  • Likely Quarternary Molecular Structure file(s) for 2VDL
  • Structure Factors (753 Kb)
  • Retrieve 2VDL in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VDL from S2C, [Save to disk]
  • Re-refined 2vdl structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2VDL 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 2VDL
  • 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 2VDL, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vdl_H] [2vdl_A] [2vdl_L] [2vdl_B] [2vdl]
  • SWISS-PROT database: [P01837] [P08514] [P05106]
  • Domain organization of [IGKC_MOUSE] [ITA2B_HUMAN] [ITB3_HUMAN] by SWISSPFAM
  • Domains found in 2VDL: [IG_like] [IGv] [INB] [Int_alpha] [PSI] [VWA ] by SMART
    • Other resources with information on 2VDL
  • Community annotation for 2VDL at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

    • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science