6YJV

Crystal structure of unliganded MGAT5 (alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase V) luminal domain with a Lys329-Ile345 loop truncation, in complex with UDP-2-deoxy-2-fluoroglucose and biantennary pentasaccharide M592

• PDB DOI: https://doi.org/10.2210/pdb6YJV/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: 1.70 Å
• R-Value Free: 0.211 
• R-Value Work: 0.175 

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: 120.92 kDa 
• Atom Count: 8,834 
• Modelled Residue Count: 1,006 
• Deposited Residue Count: 1,030 
• 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]	515	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
PHAROS:  Q09328 GTEx:  ENSG00000152127

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose	C [auth A]	4		N/A
Glycosylation Resources
GlyTouCan:  G75407YI GlyCosmos:  G75407YI GlyGen:  G75407YI

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose	D [auth B]	2		N/A
Glycosylation Resources
GlyTouCan:  G85856KC GlyCosmos:  G85856KC GlyGen:  G85856KC

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U2F (Subject of Investigation/LOI)	F [auth AAA], K [auth BBB]	URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE C15 H23 F N2 O16 P2 NGTCPFGWXMBZEP-NQQHDEILSA-N
SO4	G [auth AAA], H [auth AAA], I [auth AAA], L [auth BBB], M [auth BBB], N [auth BBB]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	E [auth AAA], J [auth BBB]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.211 
• R-Value Work: 0.175 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.52	α = 108.42
b = 69.21	β = 92.25
c = 90.65	γ = 106.54

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
REFMAC	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
• Version 1.2: 2024-10-09
  Changes: Structure summary