6SMQ Membrane Protein date Aug 22, 2019
title Structure Of The Ragab Peptide Importer In The 'Open-Closed'
authors J.B.R.White, N.A.Ranson, B.Van Den Berg
compound source
Molecule: Lipoprotein Ragb
Chain: A, D
 Organism_scientific: Porphyromonas Gingivalis (Strain Atcc W83);
Organism_taxid: 242619
Strain: Atcc Baa-308 W83

Molecule: Raga Protein
Chain: B
Organism_scientific: Porphyromonas Gingivalis (Strain Atcc W83);
Organism_taxid: 242619
Strain: Atcc Baa-308 W83

Molecule: Ser-Gly-Ala-Thr-Thr-Ala-Thr-Thr-Thr-Thr-Ser-Asn-S
Chain: C
Other_details: Putative Peptide Ligand
Organism_scientific: Porphyromonas Gingivalis W83
Organism_taxid: 242619
Strain: Krab

Molecule: Raga Protein
Chain: E
Organism_scientific: Porphyromonas Gingivalis (Strain Atcc W83);
Organism_taxid: 242619
Strain: Atcc Baa-308 W83
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 3.30 Å
ligand 5PL, C8E, PLM enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, D


E, B


Primary referenceStructural and functional insights into oligopeptide acquisition by the RagAB transporter from Porphyromonas gingivalis., Madej M, White JBR, Nowakowska Z, Rawson S, Scavenius C, Enghild JJ, Bereta GP, Pothula K, Kleinekathoefer U, Basle A, Ranson NA, Potempa J, van den Berg B, Nat Microbiol. 2020 May 11. pii: 10.1038/s41564-020-0716-y. doi:, 10.1038/s41564-020-0716-y. PMID:32393857
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (541 Kb) [Save to disk]
  • Biological Unit Coordinates (6smq.pdb1.gz) 535 Kb
  • LPC: Ligand-Protein Contacts for 6SMQ
  • CSU: Contacts of Structural Units for 6SMQ
  • Retrieve 6SMQ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6SMQ from S2C, [Save to disk]
    • View 6SMQ 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 6SMQ
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6smq_A] [6smq_D] [6smq_E] [6smq_B] [6smq_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6SMQ
  • Community annotation for 6SMQ at PDBWiki (http://pdbwiki.org)

    • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science