2DT3 Signaling Protein date Jul 09, 2006
title Crystal Structure Of The Complex Formed Between Goat Signall Protein And The Hexasaccharide At 2.28 A Resolution
authors J.Kumar, A.S.Ethayathulla, D.B.Srivastava, N.Singh, S.Sharma, T.P
compound source
Molecule: Chitinase-3-Like Protein 1
Chain: A
Synonym: Spg-40, Mammary Gland Protein Mgp-40, Bp40
 Organism_scientific: Capra Hircus
Organism_common: Goat
Organism_taxid: 9925
Secretion: Milk Mammary Gland
symmetry Space Group: P 21 21 21
R_factor 0.196 R_Free 0.215
crystal
cell
length a length b length c angle alpha angle beta angle gamma
62.300 66.420 106.620 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.28 Å
ligand MAN, NAG enzyme
note 2DT3 supersedes 2B2Z, 1ZU6
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCarbohydrate-binding properties of goat secretory glycoprotein (SPG-40) and its functional implications: structures of the native glycoprotein and its four complexes with chitin-like oligosaccharides., Kumar J, Ethayathulla AS, Srivastava DB, Singh N, Sharma S, Kaur P, Srinivasan A, Singh TP, Acta Crystallogr D Biol Crystallogr. 2007 Apr;63(Pt 4):437-46. Epub 2007, Mar 16. PMID:17372347
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (70 Kb) [Save to disk]
  • Biological Unit Coordinates (2dt3.pdb1.gz) 65 Kb
  • LPC: Ligand-Protein Contacts for 2DT3
  • CSU: Contacts of Structural Units for 2DT3
  • Likely Quarternary Molecular Structure file(s) for 2DT3
  • Structure Factors (175 Kb)
  • Retrieve 2DT3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2DT3 from S2C, [Save to disk]
  • Re-refined 2dt3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2DT3 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 2DT3
  • 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 2DT3, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2dt3_A] [2dt3]
  • SWISS-PROT database: [Q8SPQ0]
  • Domain organization of [CH3L1_CAPHI] by SWISSPFAM
  • Domain found in 2DT3: [Glyco_18 ] by SMART
    • Other resources with information on 2DT3
  • Community annotation for 2DT3 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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