1DGH Oxidoreductase date Nov 24, 1999
title Human Erythrocyte Catalase 3-Amino-1,2,4-Triazole Complex
authors C.D.Putnam, A.S.Arvai, Y.Bourne, J.A.Tainer
compound source
Molecule: Protein (Catalase)
Chain: A, C
Ec: 1.11.1.6
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell: Erythrocyte

Molecule: Protein (Catalase)
Chain: B, 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 0.173 R_Free 0.210
crystal
cell
length a length b length c angle alpha angle beta angle gamma
84.028 140.639 231.346 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand 3AH, HEM, NDP enzyme Oxidoreductase E.C.1.11.1.6 BRENDA
related structures by homologous chain: 1DGB, 1DGG
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] (357 Kb) [Save to disk]
  • Biological Unit Coordinates (1dgh.pdb1.gz) 350 Kb
  • LPC: Ligand-Protein Contacts for 1DGH
  • CSU: Contacts of Structural Units for 1DGH
  • Likely Quarternary Molecular Structure file(s) for 1DGH
  • Structure Factors (2803 Kb)
  • Retrieve 1DGH in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1DGH from S2C, [Save to disk]
  • Re-refined 1dgh structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1DGH 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 1DGH
  • 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 1DGH, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1dgha_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1dghb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1dghc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1dghd_, region D [Jmol] [rasmolscript] [script source]
  • Fold representative 1dgh 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: [1dgh_D] [1dgh_C] [1dgh] [1dgh_B] [1dgh_A]
  • SWISS-PROT database: [P04040]
  • Domain organization of [CATA_HUMAN] by SWISSPFAM
  • Domain found in 1DGH: [Catalase ] by SMART
  • Alignments of the sequence of 1DGH with the sequences similar proteins can be viewed for 1DGH'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 1DGH
  • Community annotation for 1DGH 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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