3RFE Cell Adhesion date Apr 06, 2011
title Crystal Structure Of Glycoprotein Gpib Ectodomain
authors P.A.Mcewan, W.Yang, K.H.Carr, X.Mo, X.Zheng, R.Li, J.Emsley
compound source
Molecule: Platelet Glycoprotein Ib Beta Chain
Chain: A, B
Fragment: Unp Residues 26-146
Synonym: Gp-Ib Beta, Gpib-Beta, Gpibb, Antigen Cd42b-Beta
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Gp1bb
Expression_system: Cricetulus Griseus
Expression_system_taxid: 10029
symmetry Space Group: P 1 21 1
R_factor 0.201 R_Free 0.224
crystal
cell
length a length b length c angle alpha angle beta angle gamma
61.506 34.764 71.532 90.00 92.15 90.00
method X-Ray Diffractionresolution 1.25 Å
ligand MG, NAG, SO4 enzyme
Primary referenceQuaternary organization of GPIb-IX complex and insights into Bernard-Soulier syndrome revealed by the structures of GPIbbeta and a GPIbbeta/GPIX chimera., McEwan PA, Yang W, Carr KH, Mo X, Zheng X, Li R, Emsley J, Blood. 2011 Nov 10;118(19):5292-301. Epub 2011 Sep 8. PMID:21908432
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (51 Kb) [Save to disk]
  • Biological Unit Coordinates (3rfe.pdb1.gz) 23 Kb
  • Biological Unit Coordinates (3rfe.pdb2.gz) 24 Kb
  • LPC: Ligand-Protein Contacts for 3RFE
  • CSU: Contacts of Structural Units for 3RFE
  • Structure Factors (1186 Kb)
  • Retrieve 3RFE in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3RFE from S2C, [Save to disk]
  • Re-refined 3rfe structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3RFE 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 3RFE
  • 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 3RFE, from MSDmotif at EBI
  • Fold representative 3rfe from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3rfe] [3rfe_A] [3rfe_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3RFE: [LRRCT] [LRRNT ] by SMART
  • Other resources with information on 3RFE
  • Community annotation for 3RFE at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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