9WE5 | pdb_00009we5

UDP-Glucose-bound UgtP with deletion of Pro48-Met91 and insertion of a Ser-Ser-Ser linker

PDB DOI: https://doi.org/10.2210/pdb9WE5/pdb

Classification: TRANSFERASE
Organism(s): Bacillus subtilis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-08-19 Released: 2026-08-26
Deposition Author(s): Fujishiro, T.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.70 Å
R-Value Free:
0.310 (Depositor), 0.325 (DCC)
R-Value Work:
0.230 (Depositor), 0.230 (DCC)

Starting Model: in silico
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Ligand Structure Quality Assessment

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

Literature

Structure of dimer form of UgtP

Fujishiro, T., Matsuoka, S.

To be published.

Macromolecule Content

Total Structure Weight: 80.06 kDa
Atom Count: 5,201
Modeled Residue Count: 648
Deposited Residue Count: 698
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Processive diacylglycerol beta-glucosyltransferase	A, B	349	Bacillus subtilis	Mutation(s): 0 Gene Names: ugtP, ypfP, BSU21920 EC: 2.4.1.315
UniProt
Find proteins for P54166 (Bacillus subtilis (strain 168)) Explore P54166 Go to UniProtKB: P54166
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P54166
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
660 (Subject of Investigation/LOI) Query on 660 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-[[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]methyl]phosphinic acid C₁₆ H₂₆ N₂ O₁₆ P₂ WUPLBUVQIJIOHV-RIDHHKDKSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.70 Å
R-Value Free: 0.310 (Depositor), 0.325 (DCC)
R-Value Work: 0.230 (Depositor), 0.230 (DCC)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.12	α = 90
b = 64.08	β = 107.234
c = 110.66	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-08-26

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2026-08-26
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.