2VDN	Cell Adhesion Immune System	date	Oct 10, 2007
title	Re-Refinement Of Integrin Alphaiibbeta3 Headpiece Bound To A Eptifibatide
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_common: Chinese Hamster 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_common: Chinese Hamster Expression_system_taxid: 10029 Expression_system_cell_line: Lec 3.2.8.1 Expression_system_vector_type: Plasmid
Molecule: Eptifibatide Chain: C Synonym: Mpt Hrg Gly Asp Trp Pro Cys Nh2 Engineered: Yes		Synthetic: Yes Organism_scientific: Synthetic Construct Organism_taxid: 32630
Molecule: Monoclonal Antibody 10e5 Heavy Chain Chain: H		Organism_scientific: Mus Musculus Organism_common: House Mouse Organism_taxid: 10090 Strain: Balbc Cell_line: 10e5 Hybridoma
Molecule: Monoclonal Antibody 10e5 Light Chain Chain: L		Organism_scientific: Mus Musculus Organism_common: House Mouse Organism_taxid: 10090 Strain: Balbc Cell_line: 10e5 Hybridoma
symmetry	Space Group: P 32 2 1	R_factor 0.163 R_Free 0.213
crystal cell	length a length b length c angle alpha angle beta angle gamma 149.593 149.593 175.683 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.90 Å
ligand	CA, GOL, HRG, MAN, MG, MPT, NAG, NH2	enzyme
note	2VDN supersedes 1TY6
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] (231 Kb) [Save to disk] Biological Unit Coordinates (2vdn.pdb1.gz) 218 Kb LPC: Ligand-Protein Contacts for 2VDN CSU: Contacts of Structural Units for 2VDN Likely Quarternary Molecular Structure file(s) for 2VDN Structure Factors (646 Kb) Retrieve 2VDN in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2VDN from S2C, [Save to disk] Re-refined 2vdn structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2VDN 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 2VDN

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 2VDN, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2vdn_C] [2vdn_B] [2vdn] [2vdn_L] [2vdn_H] [2vdn_A] SWISS-PROT database: [P01837] [P08514] [P05106] Domain organization of [IGKC_MOUSE] [ITA2B_HUMAN] [ITB3_HUMAN] by SWISSPFAM Domains found in 2VDN: [IG_like] [IGv] [INB] [Int_alpha] [PSI] [VWA ] by SMART

Other resources with information on 2VDN

Community annotation for 2VDN at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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