1V5H Oxygen Storage Transport date Nov 23, 2003
title Crystal Structure Of Human Cytoglobin (Ferric Form)
authors H.Sugimoto, M.Makino, H.Sawai, N.Kawada, K.Yoshizato, Y.Shiro, Riken Structural Genomicsproteomics Initiative (Rsgi)
compound source
Molecule: Cytoglobin
Chain: A
Synonym: Histoglobin, Hgb, Stellate Cell Activation- Associated Protein;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cygb, Stap
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-15b
symmetry Space Group: P 32 2 1
R_factor 0.248 R_Free 0.250
crystal
cell
length a length b length c angle alpha angle beta angle gamma
74.401 74.401 59.634 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.40 Å
ligand HEM enzyme
related structures by homologous chain: 1UMO, 1URY
Gene
Ontology
ChainFunctionProcessComponent
A
  • peroxidase activity
  • fatty acid peroxidase activi...


  • Primary referenceStructural basis of human cytoglobin for ligand binding., Sugimoto H, Makino M, Sawai H, Kawada N, Yoshizato K, Shiro Y, J Mol Biol 2004 Jun 11;339(4):873-85. PMID:15165856
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (32 Kb) [Save to disk]
  • Biological Unit Coordinates (1v5h.pdb1.gz) 54 Kb
  • LPC: Ligand-Protein Contacts for 1V5H
  • CSU: Contacts of Structural Units for 1V5H
  • Likely Quarternary Molecular Structure file(s) for 1V5H
  • Structure Factors (56 Kb)
  • Retrieve 1V5H in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1V5H from S2C, [Save to disk]
  • Re-refined 1v5h structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1V5H 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 1V5H
  • 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 1V5H, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1v5ha_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1v5h from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1v5h_A] [1v5h]
  • 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 1V5H
  • Community annotation for 1V5H 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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