2VDL Re-refinement of Integrin AlphaIIbBeta3 Headpiece date
authors Springer, T.A., Zhu, J., Xiao, T.
compound source
R_Free 0.191
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


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.

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