1DGB Oxidoreductase date Nov 23, 1999
title Human Erythrocyte Catalase
authors C.D.Putnam, A.S.Arvai, Y.Bourne, J.A.Tainer
compound source
Molecule: Catalase
Chain: A, B, C, D
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell: Erythrocyte
symmetry Space Group: P 21 21 21
R_factor 0.172 R_Free 0.227
length a length b length c angle alpha angle beta angle gamma
83.497 139.934 227.891 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand HEM, NDP enzyme Oxidoreductase E.C. BRENDA
related structures by homologous chain: 1DGH, 4BLC
A, D, C, B
  • catalase activity
  • peroxidase activity
  • antioxidant activity

  • Primary referenceActive and inhibited human catalase structures: ligand and NADPH binding and catalytic mechanism., Putnam CD, Arvai AS, Bourne Y, Tainer JA, J Mol Biol 2000 Feb 11;296(1):295-309. PMID:10656833
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (352 Kb) [Save to disk]
  • Biological Unit Coordinates (1dgb.pdb1.gz) 345 Kb
  • LPC: Ligand-Protein Contacts for 1DGB
  • CSU: Contacts of Structural Units for 1DGB
  • Likely Quarternary Molecular Structure file(s) for 1DGB
  • Structure Factors (1087 Kb)
  • Retrieve 1DGB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1DGB from S2C, [Save to disk]
  • Re-refined 1dgb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1DGB 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 1DGB
  • 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 1DGB, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1dgba_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1dgbb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1dgbc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1dgbd_, region D [Jmol] [rasmolscript] [script source]
  • Fold representative 1dgb from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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: [1dgb_B] [1dgb_C] [1dgb] [1dgb_D] [1dgb_A]
  • SWISS-PROT database: [P04040]
  • Domain organization of [CATA_HUMAN] by SWISSPFAM
  • Domain found in 1DGB: [Catalase ] by SMART
  • Other resources with information on 1DGB
  • Community annotation for 1DGB 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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