2G5R Cell Adhesion date Feb 23, 2006
title Crystal Structure Of Siglec-7 In Complex With Methyl-9-(Amin Amino)-9-Deoxyneu5ac (Oxamido-Neu5ac)
authors H.Attrill, P.R.Crocker, D.M.Van Aalten
compound source
Molecule: Sialic Acid-Binding Ig-Like Lectin 7
Chain: A
Fragment: N-Terminal Domain
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: Cho Lec1
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pdef
symmetry Space Group: P 41 21 2
R_factor 0.213 R_Free 0.228
crystal
cell
length a length b length c angle alpha angle beta angle gamma
52.928 52.928 93.236 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.60 Å
ligand CYS, NAG, NXD enzyme
note 2G5R is a representative structure
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] (27 Kb) [Save to disk]
  • Biological Unit Coordinates (2g5r.pdb1.gz) 22 Kb
  • LPC: Ligand-Protein Contacts for 2G5R
  • CSU: Contacts of Structural Units for 2G5R
  • Likely Quarternary Molecular Structure file(s) for 2G5R
  • Structure Factors (122 Kb)
  • Retrieve 2G5R in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2G5R from S2C, [Save to disk]
  • Re-refined 2g5r structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2G5R 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 2G5R
  • 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 2G5R, from MSDmotif at EBI
  • Fold representative 2g5r from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2g5r] [2g5r_A]
  • SWISS-PROT database: [Q9Y286]
  • Domain organization of [SIGL7_HUMAN] by SWISSPFAM
  • Domain found in 2G5R: [IG ] by SMART
  • Other resources with information on 2G5R
  • Community annotation for 2G5R 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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