2VDL	Cell Adhesion Immune System	date	Oct 10, 2007
title	Re-Refinement Of Integrin Alphaiibbeta3 Headpiece
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
symmetry	Space Group: P 32 2 1	R_factor 0.144 R_Free 0.191
crystal cell	length a length b length c angle alpha angle beta angle gamma 148.927 148.927 176.398 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.75 Å
ligand	CA, CAC, GOL, MAN, MG, NAG	enzyme
note	2VDL supersedes 1TXV
Gene Ontology	Chain Function Process Component A B
Primary reference	Structural 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)

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