5VEB Immune System date Apr 04, 2017
title Crystal Structure Of A Fab Binding To Extracellular Domain 5 Cadherin-6
authors X.Zhu, C.U.Bialucha, A.London, K.Clark, T.Hu
compound source
Molecule: Anti-Cdh6 Fab Heavy Chain
Chain: A, H
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Anti-Cdh6 Fab Light Chain
Chain: B, L

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Cadherin-6
Chain: X, Y
Synonym: Kidney Cadherin,K-Cadherin

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 21 21 21
R_factor 0.212 R_Free 0.252
crystal
cell
length a length b length c angle alpha angle beta angle gamma
78.829 88.855 186.730 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.34 Å
Gene
Ontology
ChainFunctionProcessComponent
X, Y


Primary referenceDiscovery and Optimization of HKT288, a Cadherin-6-Targeting ADC for the Treatment of Ovarian and Renal Cancers., Bialucha CU, Collins SD, Li X, Saxena P, Zhang X, Durr C, Lafont B, Prieur P, Shim Y, Mosher R, Lee D, Ostrom L, Hu T, Bilic S, Rajlic IL, Capka V, Jiang W, Wagner JP, Elliott G, Veloso A, Piel JC, Flaherty MM, Mansfield KG, Meseck EK, Rubic-Schneider T, London AS, Tschantz WR, Kurz M, Nguyen D, Bourret A, Meyer MJ, Faris JE, Janatpour MJ, Chan VW, Yoder NC, Catcott KC, McShea MA, Sun X, Gao H, Williams J, Hofmann F, Engelman JA, Ettenberg SA, Sellers WR, Lees E, Cancer Discov. 2017 Sep;7(9):1030-1045. doi: 10.1158/2159-8290.CD-16-1414. Epub, 2017 May 19. PMID:28526733
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (179 Kb) [Save to disk]
  • Biological Unit Coordinates (5veb.pdb1.gz) 90 Kb
  • Biological Unit Coordinates (5veb.pdb2.gz) 89 Kb
  • CSU: Contacts of Structural Units for 5VEB
  • Structure Factors (2382 Kb)
  • Retrieve 5VEB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5VEB from S2C, [Save to disk]
  • Re-refined 5veb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5VEB 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 5VEB
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5veb from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5veb_A] [5veb_B] [5veb_H] [5veb_L] [5veb_X] [5veb_Y]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5VEB
  • Community annotation for 5VEB at PDBWiki (http://pdbwiki.org)

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