9KPX | pdb_00009kpx

UDP-glycosyltransferase TsUGT1 with UDP and 3-Glc-30-S-Glc-GA

PDB DOI: https://doi.org/10.2210/pdb9KPX/pdb

Classification: TRANSFERASE
Organism(s): Trifolium subterraneum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-11-24 Released: 2025-11-26
Deposition Author(s): Feng, X., Sun, Q., Meng, L.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free:
0.209 (Depositor), 0.222 (DCC)
R-Value Work:
0.155 (Depositor), 0.175 (DCC)
R-Value Observed:
0.158 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Investigation of the bond cleavage mechanism of UDP-glycosyltransferase

Feng, X., Sun, Q., Meng, L.

To be published.

Macromolecule Content

Total Structure Weight: 217.37 kDa
Atom Count: 15,284
Modeled Residue Count: 1,884
Deposited Residue Count: 1,884
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyltransferase	A, B, C, D	471	Trifolium subterraneum	Mutation(s): 0 Gene Names: TSUD_196840 EC: 2.4.1
UniProt
Find proteins for A0A2Z6NA72 (Trifolium subterraneum) Explore A0A2Z6NA72 Go to UniProtKB: A0A2Z6NA72
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2Z6NA72
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1L68 (Subject of Investigation/LOI) Query on A1L68 Download:Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain M [auth C] SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain Q [auth D] MOL2 format, chain M [auth C] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain Q [auth D] mmCIF format, chain M [auth C] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A], I [auth B], M [auth C], Q [auth D]	(2~{S},4~{a}~{S},6~{a}~{R},6~{a}~{S},6~{b}~{R},8~{a}~{R},10~{S},12~{a}~{R},14~{b}~{R})-2,4~{a},6~{a},6~{b},9,9,12~{a}-heptamethyl-10-oxidanyl-13-oxidanylidene-3,4,5,6,6~{a},7,8,8~{a},10,11,12,14~{b}-dodecahydro-1~{H}-picene-2-carbothioic S-acid C₃₀ H₄₆ O₃ S SOGZTSGQAUOWBG-ZEYMVYSOSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain Q [auth D]
UDP Query on UDP Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain P [auth C] SDF format, chain T [auth D] SDF format, chain L [auth B] MOL2 format, chain H [auth A] MOL2 format, chain P [auth C] MOL2 format, chain T [auth D] MOL2 format, chain L [auth B] mmCIF format, chain H [auth A] mmCIF format, chain P [auth C] mmCIF format, chain T [auth D] mmCIF format, chain L [auth B]	H [auth A], L [auth B], P [auth C], T [auth D]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain T [auth D] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain T [auth D]
BMA (Subject of Investigation/LOI) Query on BMA Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain N [auth C] SDF format, chain S [auth D] SDF format, chain R [auth D] SDF format, chain O [auth C] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain N [auth C] MOL2 format, chain S [auth D] MOL2 format, chain R [auth D] MOL2 format, chain O [auth C] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain N [auth C] mmCIF format, chain S [auth D] mmCIF format, chain R [auth D] mmCIF format, chain O [auth C] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A]	F [auth A] G [auth A] J [auth B] K [auth B] N [auth C] F [auth A], G [auth A], J [auth B], K [auth B], N [auth C], O [auth C], R [auth D], S [auth D]	beta-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-RWOPYEJCSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D]