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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.211 (Depositor), 0.220 (DCC)
R-Value Work:
0.175 (Depositor), 0.180 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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

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

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q09328
Sequence Annotations Expand
Reference Sequence LOADING

Oligosaccharides

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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	Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth 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	Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
Glycosylation Resources
GlyTouCan: G85856KC GlyCosmos: G85856KC GlyGen: G85856KC

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
U2F (Subject of Investigation/LOI) Query on U2F Download Ideal Coordinates CCD File SDF format, chain F [auth AAA] SDF format, chain K [auth BBB] MOL2 format, chain F [auth AAA] MOL2 format, chain K [auth BBB] mmCIF format, chain F [auth AAA] mmCIF format, chain K [auth BBB]	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		Interactions Focus chain F [auth AAA] Focus chain K [auth BBB] Interactions & Density Focus chain F [auth AAA] Focus chain K [auth BBB]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth AAA] SDF format, chain H [auth AAA] SDF format, chain I [auth AAA] SDF format, chain L [auth BBB] SDF format, chain M [auth BBB] SDF format, chain N [auth BBB] MOL2 format, chain G [auth AAA] MOL2 format, chain H [auth AAA] MOL2 format, chain I [auth AAA] MOL2 format, chain L [auth BBB] MOL2 format, chain M [auth BBB] MOL2 format, chain N [auth BBB] mmCIF format, chain G [auth AAA] mmCIF format, chain H [auth AAA] mmCIF format, chain I [auth AAA] mmCIF format, chain L [auth BBB] mmCIF format, chain M [auth BBB] mmCIF format, chain N [auth BBB]	G [auth AAA] H [auth AAA] I [auth AAA] L [auth BBB] M [auth BBB] 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		Interactions Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain L [auth BBB] Focus chain M [auth BBB] Focus chain N [auth BBB] Interactions & Density Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain L [auth BBB] Focus chain M [auth BBB] Focus chain N [auth BBB]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth AAA] SDF format, chain J [auth BBB] MOL2 format, chain E [auth AAA] MOL2 format, chain J [auth BBB] mmCIF format, chain E [auth AAA] mmCIF format, chain J [auth BBB]	E [auth AAA], J [auth BBB]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth AAA] Focus chain J [auth BBB] Interactions & Density Focus chain E [auth AAA] Focus chain J [auth BBB]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.211 (Depositor), 0.220 (DCC)
R-Value Work: 0.175 (Depositor), 0.180 (DCC)

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

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-08-05

Deposition Author(s):

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

Revision History (Full details and data files)

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