1DKE Oxygen Storage Transport date Dec 07, 1999
title Ni Beta Heme Human Hemoglobin
authors S.Bruno, S.Bettatti, A.Mozzarelli, M.Bolognesi, D.Deriu, C.Rosano A.Tsuneshige, T.Yonetani, E.R.Henry
compound source
Molecule: Hemoglobin: Alpha Chain
Chain: A, C
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Hemoglobin: Beta Chain
Chain: B, D
Other_details: Beta Heme Contains Ni+2 Ion
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 1 21 1
R_factor 0.200 R_Free 0.280
crystal
cell
length a length b length c angle alpha angle beta angle gamma
55.720 81.400 63.150 90.00 97.81 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand HEM, SO4 enzyme
related structures by homologous chain: 1HGA, 1HGC, 1Y4B, 1Y7G
Gene
Ontology
ChainFunctionProcessComponent
A, C
  • peroxidase activity


    • D, B
  • peroxidase activity


    • Primary referenceOxygen binding by alpha(Fe2+)2beta(Ni2+)2 hemoglobin crystals., Bruno S, Bettati S, Manfredini M, Mozzarelli A, Bolognesi M, Deriu D, Rosano C, Tsuneshige A, Yonetani T, Henry ER, Protein Sci 2000 Apr;9(4):683-92. PMID:10794410
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (103 Kb) [Save to disk]
  • Biological Unit Coordinates (1dke.pdb1.gz) 97 Kb
  • LPC: Ligand-Protein Contacts for 1DKE
  • CSU: Contacts of Structural Units for 1DKE
  • Likely Quarternary Molecular Structure file(s) for 1DKE
  • Retrieve 1DKE in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1DKE from S2C, [Save to disk]
    • View 1DKE 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 1DKE
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1DKE, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1dkea_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1dkeb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1dkec_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1dked_, 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: [1dke_B] [1dke_A] [1dke_C] [1dke] [1dke_D]
  • 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 1DKE
  • Community annotation for 1DKE at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Domain movements in 1DKE from the Database of Macromolecular Movements.
  • Images from IMB Jena Image Library of Biological Macromolecules.

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