5VEB

Crystal structure of a Fab binding to extracellular domain 5 of Cadherin-6

• PDB DOI: https://doi.org/10.2210/pdb5VEB/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2017-04-04 Released: 2017-06-07 
• Deposition Author(s): Zhu, X., Bialucha, C.U., London, A., Clark, K., Hu, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free: 0.252 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 123.03 kDa 
• Atom Count: 8,497 
• Modelled Residue Count: 1,084 
• Deposited Residue Count: 1,130 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-CDH6 Fab heavy chain	A, C [auth H]	225	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for S6B291 (Homo sapiens) Explore S6B291  Go to UniProtKB:  S6B291

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-CDH6 Fab light chain	B, D [auth L]	215	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01834 (Homo sapiens) Explore P01834  Go to UniProtKB:  P01834
PHAROS:  P01834

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cadherin-6	E [auth X], F [auth Y]	125	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P55285 (Homo sapiens) Explore P55285  Go to UniProtKB:  P55285
PHAROS:  P55285 GTEx:  ENSG00000113361

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A2G	H [auth X], I [auth X], J [auth Y], K [auth Y]	2-acetamido-2-deoxy-alpha-D-galactopyranose C8 H15 N O6 OVRNDRQMDRJTHS-CBQIKETKSA-N
SIN	G [auth A]	SUCCINIC ACID C4 H6 O4 KDYFGRWQOYBRFD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free: 0.252 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.829	α = 90
b = 88.855	β = 90
c = 186.73	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-06-07 
Deposition Author(s): Zhu, X., Bialucha, C.U., London, A., Clark, K., Hu, T.

Revision History  

• Version 1.0: 2017-06-07
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary