9IMI | pdb_00009imi

Crystal structure of UGT94BY1 in complex with UDP

PDB DOI: https://doi.org/10.2210/pdb9IMI/pdb

Classification: TRANSFERASE
Organism(s): Platycodon grandiflorus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-07-03 Released: 2025-07-09
Deposition Author(s): Jiang, Z., Yuan, Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.237 (Depositor), 0.236 (DCC)
R-Value Work:
0.195 (Depositor), 0.196 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: in silico
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Ligand Structure Quality Assessment

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

Literature

Functional Characterization and Structure Basis Provide Molecular Mechanisms of UGT94BY1 for Branched-Chain Glycoside Biosynthesis

Jiang, Z., Yuan, Y.

To be published.

Macromolecule Content

Total Structure Weight: 53.09 kDa
Atom Count: 3,560
Modeled Residue Count: 428
Deposited Residue Count: 465
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyltransferase	A	465	Platycodon grandiflorus	Mutation(s): 0 EC: 2.4.1
UniProt
Find proteins for A0A9Y1LBL2 (Platycodon grandiflorus) Explore A0A9Y1LBL2 Go to UniProtKB: A0A9Y1LBL2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A9Y1LBL2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 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 B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.237 (Depositor), 0.236 (DCC)
R-Value Work: 0.195 (Depositor), 0.196 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.47	α = 90
b = 71.469	β = 90
c = 102.488	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
autoPROC	data reduction
autoPROC	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-07-09

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	82173926

Revision History (Full details and data files)

Version 1.0: 2025-07-09
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.