5NBD Transport Protein date Mar 01, 2017
title Pglk Flippase In Complex With Inhibitory Nanobody
authors C.Perez, E.Pardon, J.Steyaert, K.P.Locher
compound source
Molecule: Wlab Protein
Chain: A, B
Engineered: Yes
Mutation: Yes
 Organism_scientific: Campylobacter Jejuni
Organism_taxid: 197
Gene: Wlab
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_vector_type: Plasmid

Molecule: Nanobody
Chain: C
Engineered: Yes
Organism_scientific: Lama Glama
Organism_common: Llama
Organism_taxid: 9844
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_vector_type: Plasmid
symmetry Space Group: P 2 21 21
R_factor 0.311 R_Free 0.335
crystal
cell
length a length b length c angle alpha angle beta angle gamma
84.340 142.660 199.480 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.90 Å
ligand ADP enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • lipopolysaccharide-transport...


    • Primary referenceStructural basis of inhibition of lipid-linked oligosaccharide flippase PglK by a conformational nanobody., Perez C, Kohler M, Janser D, Pardon E, Steyaert J, Zenobi R, Locher KP, Sci Rep. 2017 Apr 19;7:46641. doi: 10.1038/srep46641. PMID:28422165
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (209 Kb) [Save to disk]
  • Biological Unit Coordinates (5nbd.pdb1.gz) 204 Kb
  • LPC: Ligand-Protein Contacts for 5NBD
  • CSU: Contacts of Structural Units for 5NBD
  • Structure Factors (456 Kb)
  • Retrieve 5NBD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5NBD from S2C, [Save to disk]
  • Re-refined 5nbd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5NBD 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 5NBD
  • 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: [5nbd_B] [5nbd] [5nbd_A] [5nbd_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5NBD
  • Community annotation for 5NBD at PDBWiki (http://pdbwiki.org)

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