5T6P Immune System date Sep 01, 2016
title Crystal Structure Of Therapeutic Mab Ar20.5 In Complex With Peptide
authors C.L.Brooks, M.Movahedin
compound source
Molecule: Fab Fragment Ar20.5 - Light Chain
Chain: A, C
Fragment: Antibody Fab Fragment
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_taxid: 10090
Expression_system: Mus Musculus
Expression_system_taxid: 10090
Expression_system_cell_line: Hybridoma, Ar20.5

Molecule: Fab Fragment - Heavy Chain
Chain: B, D
Fragment: Muc1 Peptide Apdtrpap
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_taxid: 10090
Expression_system: Mus Musculus
Expression_system_taxid: 10090
Expression_system_cell_line: Hybridoma Ar20.5

Molecule: Muc1 Peptide Fragment
Chain: E, F
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
symmetry Space Group: P 31 2 1
R_factor 0.221 R_Free 0.232
crystal
cell
length a length b length c angle alpha angle beta angle gamma
69.700 69.700 363.430 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.97 Å
Primary referenceGlycosylation of MUC1 influences the binding of a therapeutic antibody by altering the conformational equilibrium of the antigen., Movahedin M, Brooks TM, Supekar NT, Gokanapudi N, Boons GJ, Brooks CL, Glycobiology. 2016 Dec 26. pii: cww131. doi: 10.1093/glycob/cww131. PMID:28025250
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (416 Kb) [Save to disk]
  • Biological Unit Coordinates (5t6p.pdb1.gz) 204 Kb
  • Biological Unit Coordinates (5t6p.pdb2.gz) 205 Kb
  • CSU: Contacts of Structural Units for 5T6P
  • Structure Factors (1621 Kb)
  • Retrieve 5T6P in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5T6P from S2C, [Save to disk]
  • Re-refined 5t6p structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5T6P 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 5T6P
  • 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: [5t6p_A] [5t6p_B] [5t6p_E] [5t6p] [5t6p_D] [5t6p_F] [5t6p_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5T6P
  • Community annotation for 5T6P at PDBWiki (http://pdbwiki.org)

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