5EJ8 Transferase date Nov 01, 2015
title Ecmend-Thdp-Mn2+ Complex Structure Soaked With 2-Ketoglutara Min
authors H.G.Song, C.Dong, Y.Z.Chen, Y.R.Sun, Z.H.Guo
compound source
Molecule: 2-Succinyl-5-Enolpyruvyl-6-Hydroxy-3-Cyclohexene- Carboxylate Synthase;
Chain: A, B, C, D, E, F, G, H
Synonym: Thdp-Dependent Emzyme Mend,Sephchc Synthase,Menaqu Biosynthesis Protein Mend;
Ec: 2.2.1.9
Engineered: Yes
Organism_scientific: Escherichia Coli K12
Organism_taxid: 83333
Strain: K12 Substr. Mg1655
Gene: Mend, B2264, Jw5374
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
symmetry Space Group: P 1
R_factor 0.133 R_Free 0.164
crystal
cell
length a length b length c angle alpha angle beta angle gamma
90.660 90.760 169.340 83.25 76.03 64.32
method X-Ray Diffractionresolution 1.34 Å
ligand EDO, FMT, GOL, MG, MN, TD6, TRS enzyme Transferase E.C.2.2.1.9 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, A, E, B, H, C, D, G


Primary referenceA thiamine-dependent enzyme utilizes an active tetrahedral intermediate in vitamin K biosynthesis., Song H, Dong C, Qin M, Chen Y, Sun Y, Liu J, Chan W, Guo Z, J Am Chem Soc. 2016 May 23. PMID:27213829
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (2399 Kb) [Save to disk]
  • Biological Unit Coordinates (5ej8.pdb1.gz) 609 Kb
  • Biological Unit Coordinates (5ej8.pdb2.gz) 600 Kb
  • Biological Unit Coordinates (5ej8.pdb3.gz) 610 Kb
  • Biological Unit Coordinates (5ej8.pdb4.gz) 606 Kb
  • LPC: Ligand-Protein Contacts for 5EJ8
  • CSU: Contacts of Structural Units for 5EJ8
  • Structure Factors (13257 Kb)
  • Retrieve 5EJ8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5EJ8 from S2C, [Save to disk]
  • Re-refined 5ej8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5EJ8 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 5EJ8
  • 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
  • Fold representative 5ej8 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ej8_B] [5ej8] [5ej8_G] [5ej8_D] [5ej8_F] [5ej8_C] [5ej8_E] [5ej8_H] [5ej8_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5EJ8
  • Community annotation for 5EJ8 at PDBWiki (http://pdbwiki.org)

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