9KPW | pdb_00009kpw

UDP-glycosyltransferase TsUGT1 with UDP

• PDB DOI: https://doi.org/10.2210/pdb9KPW/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.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.247 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: in silico

Literature

Investigation of the bond cleavage mechanism of UDP-glycosyltransferase

Feng, X., Sun, Q.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 213.98 kDa 
• Atom Count: 15,278 
• Modeled Residue Count: 1,884 
• Deposited Residue Count: 1,884 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UDP	E [auth A], F [auth B], G [auth C], H [auth D]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.247 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.746	α = 93.744
b = 89.258	β = 97.612
c = 113.182	γ = 104.312

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-26 
Deposition Author(s): Feng, X., Sun, Q.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-11-26
  Type: Initial release