1TKK Isomerase date Jun 08, 2004
title The Structure Of A Substrate-Liganded Complex Of The L-Ala- Dl-Glu Epimerase From Bacillus Subtilis
authors V.A.Klenchin, D.M.Schmidt, J.A.Gerlt, I.Rayment
compound source
Molecule: Similar To Chloromuconate Cycloisomerase
Chain: A, B, C, D, E, F, G, H
Fragment: Ykfb
Engineered: Yes
Organism_scientific: Bacillus Subtilis
Organism_taxid: 1423
Gene: Ykfb
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3)
Expression_system_plasmid: Pet17b
symmetry Space Group: P 21 21 21
R_factor 0.219 R_Free 0.285
crystal
cell
length a length b length c angle alpha angle beta angle gamma
117.400 134.600 194.900 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand ALA, GLU, MG enzyme
related structures by homologous chain: 1JPM
Gene
Ontology
ChainFunctionProcessComponent
F, A, E, B, H, C, D, G


Primary referenceEvolution of enzymatic activities in the enolase superfamily: structure of a substrate-liganded complex of the L-Ala-D/L-Glu epimerase from Bacillus subtilis., Klenchin VA, Schmidt DM, Gerlt JA, Rayment I, Biochemistry 2004 Aug 17;43(32):10370-8. PMID:15301535
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (473 Kb) [Save to disk]
  • Biological Unit Coordinates (1tkk.pdb1.gz) 466 Kb
  • LPC: Ligand-Protein Contacts for 1TKK
  • CSU: Contacts of Structural Units for 1TKK
  • Likely Quarternary Molecular Structure file(s) for 1TKK
  • Structure Factors (1407 Kb)
  • Retrieve 1TKK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1TKK from S2C, [Save to disk]
  • Re-refined 1tkk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1TKK 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 1TKK
  • 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 1TKK, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1tkka1, region A:126-358 [Jmol] [rasmolscript] [script source]
        - Domain d1tkka2, region A:2-125 [Jmol] [rasmolscript] [script source]
        - Domain d1tkkb1, region B:126-358 [Jmol] [rasmolscript] [script source]
        - Domain d1tkkb2, region B:2-125 [Jmol] [rasmolscript] [script source]
        - Domain d1tkkc1, region C:126-358 [Jmol] [rasmolscript] [script source]
        - Domain d1tkkc2, region C:2-125 [Jmol] [rasmolscript] [script source]
        - Domain d1tkkd1, region D:126-358 [Jmol] [rasmolscript] [script source]
        - Domain d1tkkd2, region D:2-125 [Jmol] [rasmolscript] [script source]
        - Domain d1tkke1, region E:126-358 [Jmol] [rasmolscript] [script source]
        - Domain d1tkke2, region E:2-125 [Jmol] [rasmolscript] [script source]
        - Domain d1tkkf1, region F:126-358 [Jmol] [rasmolscript] [script source]
        - Domain d1tkkf2, region F:2-125 [Jmol] [rasmolscript] [script source]
        - Domain d1tkkg1, region G:126-358 [Jmol] [rasmolscript] [script source]
        - Domain d1tkkg2, region G:2-125 [Jmol] [rasmolscript] [script source]
        - Domain d1tkkh1, region H:126-358 [Jmol] [rasmolscript] [script source]
        - Domain d1tkkh2, region H:2-125 [Jmol] [rasmolscript] [script source]
  • Fold representative 1tkk 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: [1tkk_H] [1tkk_B] [1tkk_E] [1tkk_G] [1tkk_D] [1tkk_F] [1tkk_C] [1tkk_A] [1tkk]
  • SWISS-PROT database: [O34508]
  • Domain organization of [AEEP_BACSU] by SWISSPFAM
  • Domain found in 1TKK: [MR_MLE ] by SMART
  • Other resources with information on 1TKK
  • Community annotation for 1TKK 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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