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
Organism_taxid: 9606
Cell: Erythrocyte
symmetry Space Group: P 21 21 21
R_factor 0.178 R_Free 0.221
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, NDP enzyme Oxidoreductase E.C.1.11.1.6 BRENDA
related structures by homologous chain: 1DGF, 1DGH
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


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] (355 Kb) [Save to disk]
  • Biological Unit Coordinates (1dgg.pdb1.gz) 348 Kb
  • LPC: Ligand-Protein Contacts for 1DGG
  • CSU: Contacts of Structural Units for 1DGG
  • Likely Quarternary Molecular Structure file(s) for 1DGG
  • Structure Factors (3077 Kb)
  • Retrieve 1DGG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1DGG from S2C, [Save to disk]
  • Re-refined 1dgg structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1DGG 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 1DGG
  • 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 1DGG, from MSDmotif at EBI
  • 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 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: [1dgg_B] [1dgg] [1dgg_D] [1dgg_A] [1dgg_C]
  • SWISS-PROT database: [P04040]
  • Domain organization of [CATA_HUMAN] by SWISSPFAM
  • Domain found in 1DGG: [Catalase ] by SMART
  • Alignments of the sequence of 1DGG with the sequences similar proteins can be viewed for 1DGG's 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
  • Community annotation for 1DGG 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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