5D4K Immune System date Aug 07, 2015
title Crystal Structure Of The Human Polymeric Ig Receptor (Pigr)
authors B.M.Stadtmueller, P.J.Bjorkman
compound source
Molecule: Polymeric Immunoglobulin Receptor
Chain: A, B
Fragment: Ectodomain (Unp Residues 19-565)
Synonym: Poly-Ig Receptor,Hepatocellular Carcinoma-Associat Tb6;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pigr
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Hek 293-6e
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ptt5
symmetry Space Group: P 1 21 1
R_factor 0.201 R_Free 0.254
crystal
cell
length a length b length c angle alpha angle beta angle gamma
61.258 242.434 63.046 90.00 114.89 90.00
method X-Ray Diffractionresolution 2.60 Å
ligand FUC, NAG, SO4 enzyme
Primary referenceThe structure and dynamics of secretory component and its interactions with polymeric immunoglobulins., Stadtmueller BM, Huey-Tubman KE, Lopez CJ, Yang Z, Hubbell WL, Bjorkman PJ, Elife. 2016 Mar 4;5. pii: e10640. doi: 10.7554/eLife.10640. PMID:26943617
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (331 Kb) [Save to disk]
  • Biological Unit Coordinates (5d4k.pdb1.gz) 165 Kb
  • Biological Unit Coordinates (5d4k.pdb2.gz) 163 Kb
  • LPC: Ligand-Protein Contacts for 5D4K
  • CSU: Contacts of Structural Units for 5D4K
  • Structure Factors (434 Kb)
  • Retrieve 5D4K in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5D4K from S2C, [Save to disk]
  • Re-refined 5d4k structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5D4K 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 5D4K
  • 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: [5d4k_B] [5d4k_A] [5d4k]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5D4K: [IG ] by SMART
  • Other resources with information on 5D4K
  • Community annotation for 5D4K at PDBWiki (http://pdbwiki.org)

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