6OOL | pdb_00006ool

Structural elucidation of the Ectodomain of mouse UNC5H2

• PDB DOI: https://doi.org/10.2210/pdb6OOL/pdb

• Classification: PROTEIN BINDING
• Organism(s): Mus musculus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2019-04-23 Released: 2020-04-29 
• Deposition Author(s): Stetefeld, J., McDougall, M.D., Loewen, P.C., Moya, A., Meier, M.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.267 (Depositor) 
• R-Value Work: 
  0.220 (Depositor) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

Structural elucidation of the Ectodomain of mouse UNC5H2

Stetefeld, J., McDougall, M.D., Loewen, P.C., Moya, A., Meier, M.

To be published.

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: 40.54 kDa 
• Atom Count: 2,110 
• Modeled Residue Count: 244 
• Deposited Residue Count: 350 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Netrin receptor UNC5B	A	350	Mus musculus	Mutation(s): 0  Gene Names: Unc5b, Unc5h2
UniProt
Find proteins for Q8K1S3 (Mus musculus) Explore Q8K1S3  Go to UniProtKB:  Q8K1S3
Glycosylation
Glycosylation Sites: 3		Go to GlyGen: Q8K1S3-1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	B	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MAN	C [auth A], D [auth A]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
CL	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.267 (Depositor) 
• R-Value Work:  0.220 (Depositor) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.051	α = 90
b = 76.89	β = 90
c = 159.01	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
MOLREP	phasing

Structure Validation

Currently 6OOL does not have a validation slider image.

Entry History & Funding Information

Deposition Data

• Released Date: 2020-04-29 
Deposition Author(s): Stetefeld, J., McDougall, M.D., Loewen, P.C., Moya, A., Meier, M.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	PJT-152935

Revision History  

• Version 1.0: 2020-04-29
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 2.2: 2024-11-20
  Changes: Structure summary