PDB-10oh: Structure of Clostridium difficile Toxin B (TcdB) glucosyltransfe...

ID or keywords:

Entry

Database: PDB / ID: 10oh

Title

Structure of Clostridium difficile Toxin B (TcdB) glucosyltransferase in complex with UDP and isofagomine analog 2-4

Components

Toxin B

Keywords

TRANSFERASE / Inhibitor / Complex

Function / homology

Function and homology information

symbiont-mediated perturbation of host actin cytoskeleton via filamentous actin depolymerization / glucosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / host cell cytosol / cysteine-type peptidase activity / host cell endosome membrane / toxin activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lipid binding / host cell plasma membrane ...
Similarity search - Function

Biological species

Clostridioides difficile (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Gilaj, N. / Wagner, A.G. / Paparella, A.S. / Schramm, V.L. / Ghosh, A.

Funding support

United States, 3items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM041916	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	AI150971	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	S10 OD020068	United States

Citation

Journal: J.Med.Chem. / Year: 2026
Title: Isofagomine Derivatives as TcdB Glucosyltransferase Inhibitors.
Authors: Shaffer, K.J. / Gilaj, N. / Wagner, A.G. / Popadynec, M. / Groom, D.P. / Hughes, L.A. / Ghosh, A. / Paparella, A. / Tyler, P.C. / Lamiable-Oulaidi, F. / Schramm, V.L.

History

Deposition	Jan 29, 2026	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 8, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	10oh.cif.gz	474.6 KB	Display	PDBx/mmCIF format
PDB format	pdb10oh.ent.gz		Display	PDB format
PDBx/mmJSON format	10oh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/0o/10oh ftp://data.pdbj.org/pub/pdb/validation_reports/0o/10oh	HTTPS FTP

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Related structure data

Related structure data	10oiC 7lou 7lov C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#138 - Jun 2011 Glucansucrase similarity (4) #156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (2) #254 - Feb 2021 Cellulose Synthase similarity (2) #141 - Sep 2011 O-GlcNAc Transferase similarity (1)

Deposited unit

A: Toxin B

B: Toxin B

hetero molecules

131 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	50.996, 118.955, 207.965
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 2 molecules AB

#1: Protein	Toxin B Mass: 64313.836 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Amino acid residues 2-543 / Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: tcdB, toxB / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pRIL References: UniProt: P18177, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases

#1: Protein

Toxin B

Mass: 64313.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Amino acid residues 2-543 / Source: (gene. exp.)

Clostridioides difficile (bacteria) / Gene: tcdB, toxB / Plasmid: pET28a / Production host:

Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pRIL
References: UniProt: P18177, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases

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Non-polymers , 7 types, 796 molecules

#2: Chemical	ChemComp-UDP / URIDINE-5'-DIPHOSPHATE Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₁₄N₂O₁₂P₂ / Comment: UDP*YM
#3: Chemical	ChemComp-A1C9K / (2R,3R,4S,5S)-6-hydrazinyl-2-(hydroxymethyl)-2,3,4,5-tetrahydropyridine-3,4,5-triol Mass: 191.185 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₃N₃O₄
#4: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#6: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#7: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO₄
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 777 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.45 Å³/Da / Density % sol: 49.84 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 0.2 M Potassium sodium tartrate tetrahydrate and 20% (w/v) Polyethylene glycol 3,350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.91976 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 8, 2025
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.91976 Å / Relative weight: 1
Reflection	Resolution: 1.85→25 Å / Num. obs: 108973 / % possible obs: 100 % / Redundancy: 1.29 % / B_iso Wilson estimate: 16.91 Å² / CC_1/2: 0.99 / CC star: 1 / R_merge(I) obs: 0.13 / R_pim(I) all: 0.04 / R_rim(I) all: 0.13 / Net I/σ(I): 9.1
Reflection shell	Resolution: 1.85→1.87 Å / Redundancy: 13.1 % / R_merge(I) obs: 0.78 / Mean I/σ(I) obs: 2.93 / Num. unique obs: 3604 / CC_1/2: 0.83 / CC star: 0.95 / R_pim(I) all: 0.35 / % possible all: 99.2

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Processing

Software

Name	Version	Classification
PHENIX	(1.21.2_5419: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.85→24.94 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.58 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2048	5516	5.06 %
R_work	0.1708	-	-
obs	0.1725	108971	100 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.85→24.94 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8885	0	144	777	9806

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	9354
X-RAY DIFFRACTION	f_angle_d	0.815	12679
X-RAY DIFFRACTION	f_dihedral_angle_d	17.149	3553
X-RAY DIFFRACTION	f_chiral_restr	0.05	1387
X-RAY DIFFRACTION	f_plane_restr	0.007	1641

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.85-1.87	0.24	186	0.2106	3418	X-RAY DIFFRACTION	100
1.87-1.89	0.2537	169	0.2118	3401	X-RAY DIFFRACTION	100
1.89-1.92	0.2496	191	0.2119	3388	X-RAY DIFFRACTION	100
1.92-1.94	0.2599	171	0.2035	3418	X-RAY DIFFRACTION	100
1.94-1.97	0.2554	195	0.1977	3408	X-RAY DIFFRACTION	100
1.97-1.99	0.2225	210	0.1909	3343	X-RAY DIFFRACTION	100
1.99-2.02	0.2305	192	0.1807	3430	X-RAY DIFFRACTION	100
2.02-2.05	0.2157	187	0.1844	3418	X-RAY DIFFRACTION	100
2.05-2.08	0.245	162	0.1744	3408	X-RAY DIFFRACTION	100
2.08-2.12	0.1968	171	0.1748	3452	X-RAY DIFFRACTION	100
2.12-2.15	0.2268	174	0.1705	3385	X-RAY DIFFRACTION	100
2.15-2.19	0.2053	185	0.1742	3418	X-RAY DIFFRACTION	100
2.19-2.24	0.2476	177	0.1718	3431	X-RAY DIFFRACTION	100
2.24-2.28	0.2162	200	0.1773	3400	X-RAY DIFFRACTION	100
2.28-2.33	0.2415	183	0.1735	3439	X-RAY DIFFRACTION	100
2.33-2.38	0.2055	187	0.1712	3401	X-RAY DIFFRACTION	100
2.38-2.44	0.1987	174	0.1657	3465	X-RAY DIFFRACTION	100
2.44-2.51	0.1977	160	0.1733	3419	X-RAY DIFFRACTION	100
2.51-2.58	0.2128	182	0.1722	3482	X-RAY DIFFRACTION	100
2.58-2.67	0.2052	172	0.1775	3438	X-RAY DIFFRACTION	100
2.67-2.76	0.2127	185	0.1715	3429	X-RAY DIFFRACTION	100
2.76-2.87	0.204	211	0.1756	3428	X-RAY DIFFRACTION	100
2.87-3	0.2285	189	0.1827	3474	X-RAY DIFFRACTION	100
3-3.16	0.2378	183	0.1885	3461	X-RAY DIFFRACTION	100
3.16-3.36	0.2115	191	0.1826	3455	X-RAY DIFFRACTION	100
3.36-3.62	0.1951	192	0.1676	3492	X-RAY DIFFRACTION	100
3.62-3.98	0.1757	188	0.1413	3495	X-RAY DIFFRACTION	100
3.98-4.55	0.1666	182	0.1424	3533	X-RAY DIFFRACTION	100
4.55-5.73	0.1542	185	0.1528	3577	X-RAY DIFFRACTION	100
5.73-24.94	0.1696	182	0.1583	3749	X-RAY DIFFRACTION	100

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.3339	0.067	-0.5416	0.3795	-0.4774	2.044	0.2545	0.0626	0.1526	0.2411	0.038	0.0599	-1.1763	-0.1864	-0.033	0.373	-0.096	-0.0065	-0.023	-0.0466	0.098	11.682	18.3406	-23.1643
2	0.6498	-0.2815	-0.0341	1.3868	0.1937	1.6601	0.0124	0.0248	-0.1444	-0.0415	-0.0445	0.2	0.2983	-0.1983	-0.0061	0.056	-0.025	0.0239	0.0772	-0.0117	0.1051	3.9841	-8.2824	8.2076
3	0.4941	-0.1076	0.0149	1.0738	0.8251	1.9693	0.0228	-0.0237	0.0364	-0.1	0.0512	-0.0824	-0.0424	0.0278	-0.0406	0.0228	0.0074	0.025	0.0671	0.0104	0.1083	10.6005	5.1436	5.8466
4	0.5183	-0.5208	0.1884	0.8996	0.2816	1.0615	-0.0061	-0.019	-0.0079	0.0344	0.063	-0.0261	0.0098	0.0559	-0.028	0.094	0.002	0.0203	0.0776	-0.0214	0.1253	14.556	2.1111	6.3186
5	0.1749	-0.245	-0.4338	1.2432	1.0315	2.0741	0.0068	-0.0143	0.0522	0.0246	0.1078	-0.0522	-0.2007	0.2346	-0.1093	0.1179	-0.0398	-0.0082	0.0878	0.0256	0.1086	22.6994	16.75	76.0548
6	1.4051	0.4956	-0.3394	1.0942	0.0564	1.0636	-0.0556	0.0941	-0.1874	-0.0422	-0.0119	-0.0024	0.268	-0.0919	0.0454	0.1942	0.014	0.0297	0.0814	-0.0187	0.0767	13.3505	-15.3714	44.738
7	1.2229	0.0457	-0.1326	0.9573	-0.9277	2.0867	-0.0061	0.209	0.1716	0.0113	-0.0158	-0.0137	0.0034	0.0611	0.0259	0.0334	0.0015	0.0231	0.1022	0.0004	0.1098	25.7268	8.0454	36.7189
8	1.0048	0.2876	-0.9481	0.5762	-0.7081	2.3362	0.0639	0.1542	0.2093	0.0833	-0.0192	-0.0982	-0.0404	0.2489	-0.0095	0.0216	-0.0059	0.0377	0.1815	0.0214	0.1517	30.4504	10.7697	42.6392
9	3.2924	1.202	0.8477	1.3503	0.3993	2.0498	-0.0766	-0.1	0.4429	-0.1101	-0.0515	0.3583	-0.1337	-0.3308	0.109	0.1119	-0.0013	-0.0026	0.1323	-0.0143	0.1405	2.2627	-3.5177	58.4249
10	2.1947	0.6377	0.0975	1.5464	0.8707	3.5347	0.1133	-0.1797	0.3474	0.009	-0.0753	0.0806	-0.2297	-0.2949	-0.0427	0.1309	-0.0024	0.0253	0.1109	-0.0308	0.1538	16.1175	10.7126	59.6724
11	2.9322	1.8775	0.364	1.3547	0.4414	0.2657	-0.2415	0.2132	-0.2309	-0.3487	0.1688	-0.067	0.2858	-0.3174	0.0815	0.3822	-0.1088	0.0259	0.3071	0.0268	0.1514	7.3729	-3.4968	32.4661

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 108 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 109 through 308 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 309 through 463 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 464 through 546 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 2 through 108 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 109 through 264 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 265 through 339 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 340 through 393 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 394 through 463 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 464 through 507 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 508 through 544 )

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