2DF3 Cell Adhesion date Feb 23, 2006
title The Structure Of Siglec-7 In Complex With Alpha(2,3)Alpha(2 Disialyl Lactotetraosyl 2-(Trimethylsilyl)Ethyl
authors H.Attrill
compound source
Molecule: Sialic Acid-Binding Ig-Like Lectin 7
Chain: A
Fragment: Ig-Like V-Type
Synonym: Siglec-7, Qa79 Membrane Protein, Adhesion Inhibito Receptor Molecule 1, Airm-1, P75, D-Siglec, Cdw328 Antigen;
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 Lec1
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pdef
symmetry Space Group: P 41 21 2
R_factor 0.195 R_Free 0.237
length a length b length c angle alpha angle beta angle gamma
53.070 53.070 92.880 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand CYS, GAL, NAG, SIA enzyme
Primary referenceThe structure of Siglec-7 in complex with sialosides: leads for rational structure-based inhibitor design., Attrill H, Takazawa H, Witt S, Kelm S, Isecke R, Brossmer R, Ando T, Ishida H, Kiso M, Crocker PR, van Aalten DM, Biochem J. 2006 Apr 20;. PMID:16623661
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (29 Kb) [Save to disk]
  • Biological Unit Coordinates (2df3.pdb1.gz) 24 Kb
  • LPC: Ligand-Protein Contacts for 2DF3
  • CSU: Contacts of Structural Units for 2DF3
  • Likely Quarternary Molecular Structure file(s) for 2DF3
  • Structure Factors (86 Kb)
  • Retrieve 2DF3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2DF3 from S2C, [Save to disk]
  • Re-refined 2df3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2DF3 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 2DF3
  • 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 2DF3, from MSDmotif at EBI
  • Fold representative 2df3 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2df3] [2df3_A]
  • SWISS-PROT database: [Q9Y286]
  • Domain organization of [SIGL7_HUMAN] by SWISSPFAM
  • Domain found in 2DF3: [IG ] by SMART
  • Other resources with information on 2DF3
  • Community annotation for 2DF3 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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