5K2M Biosynthetic Protein date May 19, 2016
title Bifunctional Lysxargx From Thermococcus Kodakarensis With L Aaa
authors A.Yoshida, T.Tomita, M.Nishiyama
compound source
Molecule: Rimk-Related Lysine Biosynthesis Protein
Chain: A, B, C, D, G, H, I, J
Engineered: Yes
Organism_scientific: Thermococcus Kodakarensis (Strain Atcc Jcm 12380 Kod1);
Organism_taxid: 69014
Strain: Atcc Baa-918 Jcm 12380 Kod1
Gene: Tk0278
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3) Codonplus Ril

Molecule: Probable Lysine Biosynthesis Protein
Chain: E, F, K, L, M, N
Engineered: Yes

Organism_scientific: Thermococcus Kodakarensis (Strain Atcc Jcm 12380 Kod1);
Organism_taxid: 69014
Strain: Atcc Baa-918 Jcm 12380 Kod1
Gene: Tk0279
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3) Codonplus Ril
symmetry Space Group: P 1 21 1
R_factor 0.180 R_Free 0.220
crystal
cell
length a length b length c angle alpha angle beta angle gamma
76.150 135.099 136.977 90.00 97.49 90.00
method X-Ray Diffractionresolution 2.18 Å
ligand ADP, MG, PO4, SO4, UN1, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, J, B, H, C, D, I, G


F, N, K, E, M, L


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (794 Kb) [Save to disk]
  • Biological Unit Coordinates (5k2m.pdb1.gz) 782 Kb
  • Biological Unit Coordinates (5k2m.pdb2.gz) 397 Kb
  • Biological Unit Coordinates (5k2m.pdb3.gz) 393 Kb
  • LPC: Ligand-Protein Contacts for 5K2M
  • CSU: Contacts of Structural Units for 5K2M
  • Structure Factors (3048 Kb)
  • Retrieve 5K2M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5K2M from S2C, [Save to disk]
  • Re-refined 5k2m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5K2M 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 5K2M
  • 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
  • Fold representative 5k2m from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5k2m_N] [5k2m_K] [5k2m_A] [5k2m_D] [5k2m_L] [5k2m_F] [5k2m_I] [5k2m] [5k2m_E] [5k2m_C] [5k2m_B] [5k2m_M] [5k2m_J] [5k2m_G] [5k2m_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5K2M
  • Community annotation for 5K2M at PDBWiki (http://pdbwiki.org)

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