2VDR Cell Adhesion Immune System date Oct 10, 2007
title Integrin Alphaiibbeta3 Headpiece Bound To A Chimeric Fibrinogen Gamma Chain Peptide, Lggakqrgdv
authors T.A.Springer, J.Zhu, T.Xiao
compound source
Molecule: Integrin Alpha-Iib
Chain: A
Fragment: Headpiece, Residues 32-483
Synonym: Platelet Membrane Glycoprotein Iib, Gpalpha Iib, G Integrin Alpha-Iib Heavy Chain;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Cricetulus Griseus
Expression_system_taxid: 10029
Expression_system_cell_line: Lec 3.2.8.1
Expression_system_vector_type: Plasmid

Molecule: Integrin Beta-3
Chain: B
Fragment: Headpiece, Residues 27-487
Synonym: Platelet Membrane Glycoprotein Iiia, Gpiiia, Cd61
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Cricetulus Griseus
Expression_system_taxid: 10029
Expression_system_cell_line: Lec 3.2.8.1
Expression_system_vector_type: Plasmid

Molecule: Monoclonal Antibody 10e5 Heavy Chain
Chain: H

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Strain: Balbc
Cell_line: 10e5 Hybridoma

Molecule: Monoclonal Antibody 10e5 Light Chain
Chain: L

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Strain: Balbc
Cell_line: 10e5 Hybridoma

Molecule: Fibrinogen
Chain: C
Fragment: Gamma Chain C-Terminal Peptide, Residues 428-437
Engineered: Yes
Mutation: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 32 2 1
R_factor 0.148 R_Free 0.193
crystal
cell
length a length b length c angle alpha angle beta angle gamma
148.328 148.328 176.793 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.40 Å
ligand CA, GOL, MAN, MG, NAG enzyme
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] (257 Kb) [Save to disk]
  • Biological Unit Coordinates (2vdr.pdb1.gz) 243 Kb
  • LPC: Ligand-Protein Contacts for 2VDR
  • CSU: Contacts of Structural Units for 2VDR
  • Likely Quarternary Molecular Structure file(s) for 2VDR
  • Structure Factors (1133 Kb)
  • Retrieve 2VDR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VDR from S2C, [Save to disk]
  • Re-refined 2vdr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2VDR 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 2VDR
  • 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 2VDR, from MSDmotif at EBI
  • Fold representative 2vdr from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vdr_L] [2vdr] [2vdr_C] [2vdr_H] [2vdr_A] [2vdr_B]
  • SWISS-PROT database: [P02679] [P01837] [P08514] [P05106]
  • Domain organization of [FIBG_HUMAN] [IGKC_MOUSE] [ITA2B_HUMAN] [ITB3_HUMAN] by SWISSPFAM
  • Domains found in 2VDR: [IGc1] [IGv] [INB] [Int_alpha] [PSI] [VWA ] by SMART
  • Other resources with information on 2VDR
  • Community annotation for 2VDR 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
    Bioinformatics Unit
    Weizmann Institute of Science