8KB7 | pdb_00008kb7

Crystal structure of UDP/mannose-bound AGO61/beta-1,4-N-Acetylglucosaminyltransferase 2 (POMGNT2)

PDB DOI: https://doi.org/10.2210/pdb8KB7/pdb

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

Deposited: 2023-08-04 Released: 2024-08-07
Deposition Author(s): Satoh, T., Umezawa, F., Yagi, H., Kato, K.
Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Ministry of Education, Culture, Sports, Science and Technology (Japan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.228 (Depositor), 0.212 (DCC)
R-Value Work:
0.191 (Depositor)
R-Value Observed:
0.193 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of UDP/mannose-bound AGO61/beta-1,4-N-Acetylglucosaminyltransferase 2 (POMGNT2)

Satoh, T., Umezawa, F., Yagi, H., Kato, K.

To be published.

Macromolecule Content

Total Structure Weight: 260.83 kDa
Atom Count: 16,869
Modeled Residue Count: 2,041
Deposited Residue Count: 2,232
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2	A, B, C, D	558	Homo sapiens	Mutation(s): 0 Gene Names: POMGNT2, AGO61, C3orf39, EOGTL, GTDC2 EC: 2.4.1.312
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NAT1 (Homo sapiens) Explore Q8NAT1 Go to UniProtKB: Q8NAT1
PHAROS: Q8NAT1 GTEx: ENSG00000144647
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8NAT1
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D	Go to GlyGen: Q8NAT1-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UDP (Subject of Investigation/LOI) Query on UDP Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain S [auth D] SDF format, chain N [auth C] SDF format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain S [auth D] MOL2 format, chain N [auth C] MOL2 format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain S [auth D] mmCIF format, chain N [auth C] mmCIF format, chain E [auth A]	E [auth A], J [auth B], N [auth C], S [auth D]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain S [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain S [auth D]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain K [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain T [auth D] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain T [auth D] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] K [auth B] O [auth C] P [auth C] F [auth A], G [auth A], K [auth B], O [auth C], P [auth C], T [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain T [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain T [auth D]
MAN (Subject of Investigation/LOI) Query on MAN Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain Q [auth C] SDF format, chain U [auth D] SDF format, chain L [auth B] MOL2 format, chain H [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain U [auth D] MOL2 format, chain L [auth B] mmCIF format, chain H [auth A] mmCIF format, chain Q [auth C] mmCIF format, chain U [auth D] mmCIF format, chain L [auth B]	H [auth A], L [auth B], Q [auth C], U [auth D]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain U [auth D] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain U [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain R [auth C] SDF format, chain M [auth B] SDF format, chain I [auth A] MOL2 format, chain V [auth D] MOL2 format, chain R [auth C] MOL2 format, chain M [auth B] MOL2 format, chain I [auth A] mmCIF format, chain V [auth D] mmCIF format, chain R [auth C] mmCIF format, chain M [auth B] mmCIF format, chain I [auth A]	I [auth A], M [auth B], R [auth C], V [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain V [auth D] Interactions & Density Focus chain I [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain V [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.228 (Depositor), 0.212 (DCC)
R-Value Work: 0.191 (Depositor)
R-Value Observed: 0.193 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.019	α = 90
b = 150.002	β = 90
c = 191.481	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
AutoSol	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-08-07

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	23gm6410010h0004
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	JP19H03361