3NID Cell Adhesion Blood Clotting date Jun 15, 2010
title The Closed Headpiece Of Integrin Alphaiib Beta3 And Its Comp An Alpahiib Beta3 -Specific Antagonist That Does Not Induce
authors J.H.Zhu, J.Q.Zhu, T.A.Springer
compound source
Molecule: Integrin Alpha-Iib
Chain: A, C
Fragment: Integrin Alpha-Iib, Residues 32-488
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
Gene: Itga2b, Gp2b, Itgab
Expression_system: Cricetulus Griseus
Expression_system_common: Chinese Hamster
Expression_system_taxid: 10029
Expression_system_cell_line: Lec 3.2.8.1
Expression_system_cell: Cho
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcdna 3.1, Pef1

Molecule: Integrin Beta-3
Chain: B, D
Fragment: Integrin Beta-3, Residues 27-497
Synonym: Platelet Membrane Glycoprotein Iiia, Gpiiia, Cd61
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Itgb3, Gp3a
Expression_system: Cricetulus Griseus
Expression_system_common: Chinese Hamster
Expression_system_taxid: 10029
Expression_system_cell_line: Lec 3.2.8.1
Expression_system_cell: Cho
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcdna 3.1, Pef1

Molecule: Monoclonal Antibody 10e5 Heavy Chain
Chain: E, H
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Strain: Balbc
Cell_line: 10e5 Hybridoma

Molecule: Monoclonal Antibody 10e5 Light Chain
Chain: F, L
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Strain: Balbc
Cell_line: 10e5 Hybridoma
symmetry Space Group: P 21 21 2
R_factor 0.179 R_Free 0.215
crystal
cell
length a length b length c angle alpha angle beta angle gamma
258.970 144.490 104.200 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand CA, GOL, MAN, MG, NAG, SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, C


D, B


Primary referenceClosed headpiece of integrin alphaIIbbeta3 and its complex with an alphaIIbbeta3-specific antagonist that does not induce opening., Zhu J, Zhu J, Negri A, Provasi D, Filizola M, Coller BS, Springer TA, Blood. 2010 Dec 2;116(23):5050-9. Epub 2010 Aug 2. PMID:20679525
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (904 Kb) [Save to disk]
  • Biological Unit Coordinates (3nid.pdb1.gz) 450 Kb
  • Biological Unit Coordinates (3nid.pdb2.gz) 445 Kb
  • LPC: Ligand-Protein Contacts for 3NID
  • CSU: Contacts of Structural Units for 3NID
  • Structure Factors (1327 Kb)
  • Retrieve 3NID in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3NID from S2C, [Save to disk]
  • Re-refined 3nid structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3NID 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 3NID
  • 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 3NID, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3nid_E] [3nid_D] [3nid_C] [3nid_H] [3nid_L] [3nid_B] [3nid_A] [3nid] [3nid_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3NID: [IG_like] [IGv] [INB] [Int_alpha] [PSI] [VWA ] by SMART
    • Other resources with information on 3NID
  • Community annotation for 3NID 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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