1DGG Oxidoreductase date Nov 24, 1999
title Human Erythrocyte Catalse Cyanide Complex
authors C.D.Putnam, A.S.Arvai, Y.Bourne, J.A.Tainer
compound source
Molecule: Catalase
Chain: A, B, C, D
Ec: 1.11.1.6
Organism_scientific: Homo Sapiens
Organism_common: Human
Cell: Erythrocyte
symmetry Space Group: P 21 21 21
R_factor 0.178
crystal
cell
length a length b length c angle alpha angle beta angle gamma
83.862 140.608 231.591 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand CYN, HEM, NDPenzyme Oxidoreductase E.C.1.11.1.6
related structures by homologous chain: 1DGF, 1DGH
similarity Belongs to the catalase family.
subunit Homotetramer.
catalytic activ. 2 h(2)o(2) = o(2) + 2 h(2)o.
subcellular loc. Peroxisomal.
gene CAT (H. sapiens)
function Occurs in almost all aerobically respiring organisms and serves to protect cells from the toxic effects of hydrogen peroxide.
Gene
Ontology
chain A: GO:0004096, GO:0004601, GO:0005777, GO:0006118, GO:0006979, GO:0016491
chain B: GO:0004096, GO:0004601, GO:0005777, GO:0006118, GO:0006979, GO:0016491
chain C: GO:0004096, GO:0004601, GO:0005777, GO:0006118, GO:0006979, GO:0016491
chain D: GO:0004096, GO:0004601, GO:0005777, GO:0006118, GO:0006979, GO:0016491
disease Acatalasemia
This disease is characterized by absence of catalase activity in red cells and is often associated with ulcerating oral lesions. Defects in cat are the cause of acatalasia [mim. 115500]; also known as acatalasemia.
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] (384 Kb) [Save to disk]
  • Biological Unit Coordinates (1dgg.pdb1.gz) 350 Kb
  • LPC: Ligand-Protein Contacts for 1DGG
  • CSU: Contacts of Structural Units for 1DGG
  • Likely Quarternary Molecular Structure file(s) for 1DGG
  • Structure Factors (r1dggsf.ent.Z) 2987 Kb
  • Retrieve 1DGG in mmCIF format [Save to disk]
  • View 1DGG in 3D
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On AstexViewer, from MSD-EBI (viewer documentation).
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  • Visual 3D analysis of 1DGG
  • STING, shows the sequence and maps the locations of sequence residues or residue ranges onto the 3D structure.
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  • GRASS (Graphical Representation and Analysis of Structure Server)
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electro 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
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1dgga_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1dggb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1dggc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1dggd_, region D [Jmol] [rasmolscript] [script source]
  • Fold representative 1dgg from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily: CATH
  • Summaries and structural analyses of PDB data files: PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1dgg_A] [1dgg_B] [1dgg_C] [1dgg_D]
  • SWISS-PROT database: [P04040]
  • Domain organization of [CATA_HUMAN] by SWISSPFAM
  • Conserved protein region description, domain view and alignment from family catalase (PF00199) of Pfam.
  • Alignments of the sequence of 1DGG with the sequences similar proteins can be viewed for classification [CATA_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [CATA_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1DGG
  • InterPro: IPR002226
  • PDBREPORT (protein verification by WHAT_CHECK procedures)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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