5D6K Transport Protein date Aug 12, 2015
title Pept - Cim
authors P.Ma, M.Caffrey
compound source
Molecule: Di-Or Tripeptide:H+ Symporter
Chain: A
Engineered: Yes
 Organism_scientific: Streptococcus Thermophilus (Strain Atc Lmg 18311);
Organism_taxid: 264199
Strain: Atcc Baa-250 Lmg 18311
Gene: Dtpt, Stu0970
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_variant: C43
symmetry Space Group: C 2 2 21
R_factor 0.216 R_Free 0.246
crystal
cell
length a length b length c angle alpha angle beta angle gamma
101.690 110.910 112.360 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand 97M, 97N, PO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceThe cubicon method for concentrating membrane proteins in the cubic mesophase., Ma P, Weichert D, Aleksandrov LA, Jensen TJ, Riordan JR, Liu X, Kobilka BK, Caffrey M, Nat Protoc. 2017 Sep;12(9):1745-1762. doi: 10.1038/nprot.2017.057. Epub 2017 Aug , 3. PMID:28771236
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (80 Kb) [Save to disk]
  • Biological Unit Coordinates (5d6k.pdb1.gz) 75 Kb
  • LPC: Ligand-Protein Contacts for 5D6K
  • CSU: Contacts of Structural Units for 5D6K
  • Structure Factors (436 Kb)
  • Retrieve 5D6K in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5D6K from S2C, [Save to disk]
  • Re-refined 5d6k structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5D6K 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 5D6K
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5d6k_A] [5d6k]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5D6K
  • Community annotation for 5D6K at PDBWiki (http://pdbwiki.org)

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