2TOD Lyase date May 18, 1999
title Ornithine Decarboxylase From Trypanosoma Brucei K69a Mutant With Alpha-Difluoromethylornithine
authors N.V.Grishin, A.L.Osterman, H.B.Brooks, M.A.Phillips, E.J.Goldsmi
compound source
Molecule: Protein (Ornithine Decarboxylase)
Chain: A, B, C, D
Ec: 4.1.1.17
Engineered: Yes
Mutation: Yes
Organism_scientific: Trypanosoma Brucei
Organism_taxid: 5691
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: B21dg3
Expression_system_cellular_location: Cytoplasm
symmetry Space Group: P 1 21 1
R_factor 0.212 R_Free 0.270
crystal
cell
length a length b length c angle alpha angle beta angle gamma
66.800 154.500 77.100 90.00 90.58 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand DMO, PLP enzyme Lyase E.C.4.1.1.17 BRENDA
related structures by homologous chain: 1F3T, 7ODC
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceX-ray structure of ornithine decarboxylase from Trypanosoma brucei: the native structure and the structure in complex with alpha-difluoromethylornithine., Grishin NV, Osterman AL, Brooks HB, Phillips MA, Goldsmith EJ, Biochemistry 1999 Nov 16;38(46):15174-84. PMID:10563800
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (249 Kb) [Save to disk]
  • Biological Unit Coordinates (2tod.pdb1.gz) 123 Kb
  • Biological Unit Coordinates (2tod.pdb2.gz) 123 Kb
  • LPC: Ligand-Protein Contacts for 2TOD
  • CSU: Contacts of Structural Units for 2TOD
  • Likely Quarternary Molecular Structure file(s) for 2TOD
  • Retrieve 2TOD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2TOD from S2C, [Save to disk]
  • View 2TOD 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 2TOD
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2TOD, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d2toda1, region A:37-43,A:284-410 [Jmol] [rasmolscript] [script source]
        - Domain d2toda2, region A:44-283 [Jmol] [rasmolscript] [script source]
        - Domain d2todb1, region B:37-43,B:284-410 [Jmol] [rasmolscript] [script source]
        - Domain d2todb2, region B:44-283 [Jmol] [rasmolscript] [script source]
        - Domain d2todc1, region C:37-43,C:284-410 [Jmol] [rasmolscript] [script source]
        - Domain d2todc2, region C:44-283 [Jmol] [rasmolscript] [script source]
        - Domain d2todd1, region D:37-43,D:284-410 [Jmol] [rasmolscript] [script source]
        - Domain d2todd2, region D:44-283 [Jmol] [rasmolscript] [script source]
  • Fold representative 2tod 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: [2tod_C] [2tod] [2tod_B] [2tod_D] [2tod_A]
  • SWISS-PROT database: [P07805]
  • Domain organization of [DCOR_TRYBB] by SWISSPFAM
  • Other resources with information on 2TOD
  • Community annotation for 2TOD 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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