1URY Oxygen Transport date Nov 12, 2003
title Cytoglobin Cavities
authors D.De Sanctis, S.Dewilde, A.Pesce, L.Moens, P.Ascenzi, T.Hankeln, T.Burmester, M.Bolognesi
compound source
Molecule: Cytoglobin
Chain: A, B
Synonym: Histoglobin, Hgb, Stellate Cell Activation- Associated-Protein, Cygb, Stap;
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.19702 R_Free 0.25442
crystal
cell
length a length b length c angle alpha angle beta angle gamma
47.848 70.524 98.728 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.4 Å
ligand FC6, HEM, XE enzyme
related structures by homologous chain: 1UX9, 1V5H
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • peroxidase activity
  • fatty acid peroxidase activi...


  • Primary referenceMapping protein matrix cavities in human cytoglobin through Xe atom binding., de Sanctis D, Dewilde S, Pesce A, Moens L, Ascenzi P, Hankeln T, Burmester T, Bolognesi M, Biochem Biophys Res Commun. 2004 Apr 16;316(4):1217-21. PMID:15044115
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (59 Kb) [Save to disk]
  • Biological Unit Coordinates (1ury.pdb1.gz) 28 Kb
  • Biological Unit Coordinates (1ury.pdb2.gz) 28 Kb
  • LPC: Ligand-Protein Contacts for 1URY
  • CSU: Contacts of Structural Units for 1URY
  • Likely Quarternary Molecular Structure file(s) for 1URY
  • Structure Factors (179 Kb)
  • Retrieve 1URY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1URY from S2C, [Save to disk]
  • Re-refined 1ury structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1URY 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 1URY
  • 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 1URY, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1urya_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1uryb_, region B [Jmol] [rasmolscript] [script source]
  • Fold representative 1ury from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1ury_A] [1ury] [1ury_B]
  • SWISS-PROT database: [Q8WWM9]
  • Belongs to the pore-forming globin (globin) family according to TCDB.
  • Domain organization of [CYGB_HUMAN] by SWISSPFAM
  • Other resources with information on 1URY
  • Community annotation for 1URY 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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