1GYK Glycoprotein date Apr 25, 2002
title Serum Amyloid P Component Co-Crystallised With Mobdg At Neut
authors D.Thompson, M.B.Pepys, I.Tickle, S.P.Wood
compound source
Molecule: Serum Amyloid P-Component
Chain: A, B, C, D, E
Synonym: Sap, 9.5s Alpha-1-Glycoprotein
Other_details: Crystallised With Mobdg
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 1 21 1
R_factor 0.186 R_Free 0.224
crystal
cell
length a length b length c angle alpha angle beta angle gamma
95.760 70.530 103.410 90.00 96.80 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand CA, CDG enzyme
related structures by homologous chain: 1LGN, 1SAC
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, E, B
  • negative regulation of monoc...

    • Primary referenceThe structures of crystalline complexes of human serum amyloid P component with its carbohydrate ligand, the cyclic pyruvate acetal of galactose., Thompson D, Pepys MB, Tickle I, Wood S, J Mol Biol 2002 Jul 26;320(5):1081-6. PMID:12126626
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (171 Kb) [Save to disk]
  • Biological Unit Coordinates (1gyk.pdb1.gz) 164 Kb
  • LPC: Ligand-Protein Contacts for 1GYK
  • CSU: Contacts of Structural Units for 1GYK
  • Likely Quarternary Molecular Structure file(s) for 1GYK
  • Structure Factors (485 Kb)
  • Retrieve 1GYK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1GYK from S2C, [Save to disk]
  • Re-refined 1gyk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1GYK 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 1GYK
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1GYK, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1gyka_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1gykb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1gykc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1gykd_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1gyke_, region E [Jmol] [rasmolscript] [script source]
  • 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: [1gyk_A] [1gyk_E] [1gyk_B] [1gyk_D] [1gyk] [1gyk_C]
  • SWISS-PROT database: [P02743]
  • Belongs to the pentraxin (pentraxin) family according to TCDB.
  • Domain organization of [SAMP_HUMAN] by SWISSPFAM
  • Domain found in 1GYK: [PTX ] by SMART
    • Other resources with information on 1GYK
  • Community annotation for 1GYK 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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