3ZDZ Cell Adhesion Immune System Peptide date Dec 03, 2012
title Integrin Alphaiib Beta3 Headpiece And Rgd Peptide Complex
authors J.H.Zhu, J.Q.Zhu, T.A.Springer
compound source
Molecule: Integrin Alpha-Iib
Chain: A, C
Fragment: Residues 32-488
Synonym: Gpalpha Iib, Gpiib, Platelet Membrane Glycoprotein
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: Cho Lec 3.2.1.8
Expression_system_vector: Pcdna3.1

Molecule: Integrin Beta-3
Chain: B, D
Fragment: Residues 27-498
Synonym: Platelet Membrane Glycoprotein Iiia, Gpiiia
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: Cho Lec 3.2.1.8
Expression_system_vector: Pef1

Molecule: 10e5 Fab Heavy Chain
Chain: E, H
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Expression_system: Mus Musculus
Expression_system_common: House Mouse
Expression_system_taxid: 10090

Molecule: 10e5 Fab Light Chain
Chain: F, L
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Expression_system: Mus Musculus
Expression_system_common: House Mouse
Expression_system_taxid: 10090

Molecule: Rgd Peptide
Chain: I, J
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 21 21 2
R_factor 0.184 R_Free 0.221
crystal
cell
length a length b length c angle alpha angle beta angle gamma
259.620 144.470 104.750 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.75 Å
ligand BMA, CA, CL, MAN, MN, NAG, SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, C


D, B


Primary referenceComplete integrin headpiece opening in eight steps., Zhu J, Zhu J, Springer TA, J Cell Biol. 2013 Jun 24;201(7):1053-68. doi: 10.1083/jcb.201212037. PMID:23798730
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1291 Kb) [Save to disk]
  • Biological Unit Coordinates (3zdz.pdb1.gz) 642 Kb
  • Biological Unit Coordinates (3zdz.pdb2.gz) 644 Kb
  • LPC: Ligand-Protein Contacts for 3ZDZ
  • CSU: Contacts of Structural Units for 3ZDZ
  • Structure Factors (1371 Kb)
  • Retrieve 3ZDZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3ZDZ from S2C, [Save to disk]
  • Re-refined 3zdz structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3ZDZ 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 3ZDZ
  • 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 3ZDZ, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3zdz_B] [3zdz_C] [3zdz_H] [3zdz_D] [3zdz_L] [3zdz] [3zdz_A] [3zdz_J] [3zdz_F] [3zdz_E] [3zdz_I]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3ZDZ: [IG_like] [IGv] [INB] [Int_alpha] [PSI] [VWA ] by SMART
  • Other resources with information on 3ZDZ
  • Community annotation for 3ZDZ at PDBWiki (http://pdbwiki.org)

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