5J5J

Crystal structure of a chimera of human Desmocollin-2 EC1 and human Desmoglein-2 EC2-EC5

• PDB DOI: https://doi.org/10.2210/pdb5J5J/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2016-04-02 Released: 2016-06-22 
• Deposition Author(s): Brasch, J., Harrison, O.J., Shapiro, L.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.29 Å
• R-Value Free: 0.285 
• R-Value Work: 0.247 
• R-Value Observed: 0.249 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 67.15 kDa 
• Atom Count: 4,644 
• Modelled Residue Count: 552 
• Deposited Residue Count: 557 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Desmocollin-2,Desmoglein-2	A	557	Homo sapiens	Mutation(s): 0  Gene Names: DSC2, CDHF2, DSC3, DSG2, CDHF5
UniProt & NIH Common Fund Data Resources
Find proteins for Q14126 (Homo sapiens) Explore Q14126  Go to UniProtKB:  Q14126
PHAROS:  Q14126 GTEx:  ENSG00000046604
Find proteins for Q02487 (Homo sapiens) Explore Q02487  Go to UniProtKB:  Q02487
PHAROS:  Q02487 GTEx:  ENSG00000134755
UniProt Groups	Q14126Q02487

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	8		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G88310KZ GlyCosmos:  G88310KZ GlyGen:  G88310KZ

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	C	6		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G82348BZ GlyCosmos:  G82348BZ GlyGen:  G82348BZ

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	H [auth A], I [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MAN	E [auth A], F [auth A], G [auth A]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
CA	J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	U [auth A], V [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.29 Å
• R-Value Free: 0.285 
• R-Value Work: 0.247 
• R-Value Observed: 0.249 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.494	α = 90
b = 87.489	β = 90
c = 218.536	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-06-22 
Deposition Author(s): Brasch, J., Harrison, O.J., Shapiro, L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM062270

Revision History  

• Version 1.0: 2016-06-22
  Type: Initial release
  
• Version 1.1: 2016-06-29
  Changes: Database references
• Version 1.2: 2016-07-13
  Changes: Database references
• Version 1.3: 2017-09-20
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.4: 2019-12-25
  Changes: Author supporting evidence, Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary