1NKO Immune System date Jan 03, 2003
title Energetic And Structural Basis Of Sialylated Oligosaccharide Recognition By The Natural Killer Cell Inhibitory Receptor P75airm1 Or Siglec-7
authors N.Dimasi, H.Attril, D.M.F.Van Aalten, L.Moretta, R.Biassoni, R.A.Mariuzza
compound source
Molecule: Sialic Acid Binding Ig-Like Lectin 7
Chain: A
Fragment: N-Terminal Igv-Like Domain Residues 19-150
Synonym: Siglec-7, Qa79 Membrane Protein, Adhesion Inhibitory Recptor Molecule-1, Airm-1, P75, D-Siglec;
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Siglec7 Or Airm1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector_type: Pt7-7
Expression_system_plasmid: P75-1d
symmetry Space Group: P 1 21 1
R_factor 0.277 R_Free 0.301
crystal
cell
length a length b length c angle alpha angle beta angle gamma
32.461 49.715 39.787 90.00 113.08 90.00
method X-Ray Diffractionresolution 1.45 Å
related structures by homologous chain: 1O7S
Primary referenceStructure of the saccharide-binding domain of the human natural killer cell inhibitory receptor p75/AIRM1., Dimasi N, Moretta A, Moretta L, Biassoni R, Mariuzza RA, Acta Crystallogr D Biol Crystallogr 2004 Feb;60(Pt 2):401-3. Epub 2004 Jan, 23. PMID:14747738
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (24 Kb) [Save to disk]
  • Biological Unit Coordinates (1nko.pdb1.gz) 21 Kb
  • CSU: Contacts of Structural Units for 1NKO
  • Likely Quarternary Molecular Structure file(s) for 1NKO
  • Structure Factors (144 Kb)
  • Retrieve 1NKO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1NKO from S2C, [Save to disk]
  • Re-refined 1nko structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1NKO 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 1NKO
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Conformational Epitope Prediction for 1NKO from the CEP Server.
  • 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 1NKO, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1nkoa_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1nko from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1nko] [1nko_A]
  • SWISS-PROT database: [Q9Y286]
  • Domain organization of [SIGL7_HUMAN] by SWISSPFAM
  • Domain found in 1NKO: [IG ] by SMART
  • Other resources with information on 1NKO
  • Community annotation for 1NKO 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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