1S5Y Oxygen Storage Transport date Jan 22, 2004
title The Crystal Structure Of Trematomus Bernacchii Hemoglobin Ox Ferricyanide
authors L.Vitagliano, G.Bonomi, A.Riccio, G.Di Prisco, G.Smulevich, L.Maz
compound source
Molecule: Hemoglobin Alpha Chain
Chain: A, C
 Organism_scientific: Trematomus Bernacchii
Organism_common: Emerald Rockcod
Organism_taxid: 40690

Molecule: Hemoglobin Beta Chain
Chain: B, D
Organism_scientific: Trematomus Bernacchii
Organism_common: Emerald Rockcod
Organism_taxid: 40690
symmetry Space Group: P 1
R_factor 0.199 R_Free 0.247
crystal
cell
length a length b length c angle alpha angle beta angle gamma
55.993 62.980 63.502 77.06 69.79 84.17
method X-Ray Diffractionresolution 2.50 Å
ligand ACE, HEM enzyme
related structures by homologous chain: 1PBX
Gene
Ontology
ChainFunctionProcessComponent
A, C


D, B


Primary referenceThe oxidation process of Antarctic fish hemoglobins., Vitagliano L, Bonomi G, Riccio A, di Prisco G, Smulevich G, Mazzarella L, Eur J Biochem 2004 May;271(9):1651-9. PMID:15096204
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (98 Kb) [Save to disk]
  • Biological Unit Coordinates (1s5y.pdb1.gz) 92 Kb
  • LPC: Ligand-Protein Contacts for 1S5Y
  • CSU: Contacts of Structural Units for 1S5Y
  • Likely Quarternary Molecular Structure file(s) for 1S5Y
  • Retrieve 1S5Y in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1S5Y from S2C, [Save to disk]
    • View 1S5Y 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 1S5Y
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1S5Y, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1s5ya_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1s5yb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1s5yc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1s5yd_, region D [Jmol] [rasmolscript] [script source]
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1s5y_B] [1s5y_D] [1s5y_C] [1s5y] [1s5y_A]
  • SWISS-PROT database: [P80043] [P80044]
  • Domain organization of [HBA_PAGBE] [HBB_PAGBE] by SWISSPFAM
    • Other resources with information on 1S5Y
  • Community annotation for 1S5Y 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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