1DKW Isomerase date Dec 08, 1999
title Crystal Structure Of Triose-Phosphate Isomerase With Modifie Substrate Binding Site
authors B.V.Norledge, A.M.Lambeir, R.A.Abagyan, A.Rottman, A.M.Fernandez V.V.Filimonov, M.G.Peter, R.K.Wierenga
compound source
Molecule: Triosephosphate Isomerase
Chain: A, B
Ec: 5.3.1.1
Engineered: Yes
Organism_scientific: Trypanosoma Brucei Brucei
Organism_taxid: 5702
Strain: Brucei
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector: Pet3a
symmetry Space Group: P 1 21 1
R_factor 0.183 R_Free 0.242
crystal
cell
length a length b length c angle alpha angle beta angle gamma
46.570 88.530 56.220 90.00 97.26 90.00
method X-Ray Diffractionresolution 2.65 Å
ligand TBU enzyme Isomerase E.C.5.3.1.1 BRENDA
related structures by homologous chain: 1ML1, 3TIM
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceModeling, mutagenesis, and structural studies on the fully conserved phosphate-binding loop (loop 8) of triosephosphate isomerase: toward a new substrate specificity., Norledge BV, Lambeir AM, Abagyan RA, Rottmann A, Fernandez AM, Filimonov VV, Peter MG, Wierenga RK, Proteins 2001 Feb 15;42(3):383-9. PMID:11151009
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (79 Kb) [Save to disk]
  • Biological Unit Coordinates (1dkw.pdb1.gz) 74 Kb
  • LPC: Ligand-Protein Contacts for 1DKW
  • CSU: Contacts of Structural Units for 1DKW
  • Likely Quarternary Molecular Structure file(s) for 1DKW
  • Structure Factors (90 Kb)
  • Retrieve 1DKW in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1DKW from S2C, [Save to disk]
  • Re-refined 1dkw structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1DKW 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 1DKW
  • 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
  • 3D motif for 1DKW, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1dkwa_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1dkwb_, region B [Jmol] [rasmolscript] [script source]
  • 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: [1dkw] [1dkw_A] [1dkw_B]
  • SWISS-PROT database: [P04789]
  • Domain organization of [TPIS_TRYBB] by SWISSPFAM
  • Other resources with information on 1DKW
  • Community annotation for 1DKW 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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