1R1Y Oxygen Transport date Sep 25, 2003
title Crystal Structure Of Deoxy-Human Hemoglobin Bassett At 1.8 A
authors O.Abdulmalik, M.K.Safo, N.B.Lerner, J.Ochotorena, Y.Dhaikin, D.J. T.Asakura
compound source
Molecule: Hemoglobin Alpha Chain
Chain: A, C
Mutation: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Tissue: Blood

Molecule: Hemoglobin Beta Chain
Chain: B, D
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Tissue: Blood
symmetry Space Group: P 1 21 1
R_factor 0.183 R_Free 0.236
crystal
cell
length a length b length c angle alpha angle beta angle gamma
62.471 82.246 53.561 90.00 100.21 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand HEM, SO4 enzyme
related structures by homologous chain: 1C7B, 1C7D, 1O1O
Gene
Ontology
ChainFunctionProcessComponent
A, C
  • peroxidase activity


    • D, B
  • peroxidase activity


    • Primary referenceCharacterization of hemoglobin bassett (alpha94Asp-->Ala), a variant with very low oxygen affinity., Abdulmalik O, Safo MK, Lerner NB, Ochotorena J, Daikhin E, Lakka V, Santacroce R, Abraham DJ, Asakura T, Am J Hematol 2004 Nov;77(3):268-76. PMID:15495251
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (107 Kb) [Save to disk]
  • Biological Unit Coordinates (1r1y.pdb1.gz) 102 Kb
  • LPC: Ligand-Protein Contacts for 1R1Y
  • CSU: Contacts of Structural Units for 1R1Y
  • Likely Quarternary Molecular Structure file(s) for 1R1Y
  • Structure Factors (282 Kb)
  • Retrieve 1R1Y in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1R1Y from S2C, [Save to disk]
  • Re-refined 1r1y structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1R1Y 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 1R1Y
  • 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 1R1Y, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1r1ya_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1r1yb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1r1yc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1r1yd_, region D [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: [1r1y_D] [1r1y_A] [1r1y_B] [1r1y] [1r1y_C]
  • SWISS-PROT database: [P69905] [P68871]
  • Belongs to the pore-forming globin (globin) family according to TCDB.
  • Belongs to the pore-forming globin (globin) family according to TCDB.
  • Domain organization of [HBA_HUMAN] [HBB_HUMAN] by SWISSPFAM
    • Other resources with information on 1R1Y
  • Community annotation for 1R1Y 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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