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		Organism_scientific: Homo Sapiens Organism_common: Human, Human Organism_taxid: 9606
Molecule: Anti-Cdh6 Fab Light Chain Chain: B, L		Organism_scientific: Homo Sapiens Organism_common: Human, Human Organism_taxid: 9606
Molecule: Anti-Cdh6 Fab Heavy Chain Chain: H		Organism_scientific: Homo Sapiens Organism_common: Human, Human Organism_taxid: 9606
Molecule: Cadherin-6 Chain: X, Y Synonym: Kidney Cadherin,K-Cadherin Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Cdh6 Expression_system: Homo Sapiens Expression_system_common: Human Expression_system_taxid: 9606 Expression_system_cell_line: Hek293
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 Diffraction	resolution	2.34 Å
ligand	A2G, SIN	enzyme
Gene Ontology	Chain Function Process Component X, Y
Primary reference	Discovery 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] (176 Kb) [Save to disk] Biological Unit Coordinates (5veb.pdb1.gz) 88 Kb Biological Unit Coordinates (5veb.pdb2.gz) 88 Kb LPC: Ligand-Protein Contacts for 5VEB 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

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: [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)

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

---