6YJR

Crystal structure of unliganded MGAT5 (alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase V) luminal domain.

• PDB DOI: https://doi.org/10.2210/pdb6YJR/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2020-04-04 Released: 2020-08-05 
• Deposition Author(s): Wu, L., Darby, J.F., Gilio, A.K., Davies, G.J.
• Funding Organization(s): European Research Council (ERC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.263 
• R-Value Work: 0.208 

Starting Model: experimental

Literature

Substrate Engagement and Catalytic Mechanisms of N-Acetylglucosaminyltransferase V

Darby, J.F., Gilio, A.K., Piniello, B., Roth, C., Blagova, E., Rovira, C., Hubbard, R.E., Davies, G.J., Wu, L.

(2020) ACS Catal 

• DOI: https://doi.org/10.1021/acscatal.0c02222

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 122.29 kDa 
• Atom Count: 8,052 
• Modelled Residue Count: 988 
• Deposited Residue Count: 1,056 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A	A [auth AAA], B [auth BBB]	528	Homo sapiens	Mutation(s): 0  Gene Names: MGAT5, GGNT5 EC: 2.4.1.155
UniProt & NIH Common Fund Data Resources
Find proteins for Q09328 (Homo sapiens) Explore Q09328  Go to UniProtKB:  Q09328
GTEx:  ENSG00000152127
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: Q09328-1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth A], D [auth B]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC GlyCosmos:  G86851RC GlyGen:  G86851RC

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth AAA]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
EDO	F [auth AAA], G [auth AAA], H [auth BBB], I [auth BBB]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.263 
• R-Value Work: 0.208 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.809	α = 90
b = 100.415	β = 90
c = 207.981	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
STARANISO	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-08-05 
Deposition Author(s): Wu, L., Darby, J.F., Gilio, A.K., Davies, G.J.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	United Kingdom	ErC-2012-AdG-322942

Revision History  

• Version 1.0: 2020-08-05
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description