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234,785 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Source Organism Taxonomy Name (Full Lineage) = "Clostridioides difficile"

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Search Summary

This query matches 343 Structures.

Refinements

Structure Determination Methodology

experimental (343)

Scientific Name of Source Organism

	Clostridioides difficile (193)
	Clostridioides difficile 630 (122)
	Clostridioides difficile R20291 (24)
	Homo sapiens (18)
	Camelidae (6)
	Lama glama (6)
	synthetic construct (6)
	Escherichia coli (4)
	Clostridioides difficile NAP07 (3)
	Clostridioides difficile QCD-32g58 (3)

More...

Taxonomy

	Bacteria (343)
	Eukaryota (35)
	other sequences (6)

Experimental Method

	X-RAY DIFFRACTION (286)
	ELECTRON MICROSCOPY (52)
	SOLUTION NMR (4)
	ELECTRON CRYSTALLOGRAPHY (1)

Polymer Entity Type

	Protein (342)
	DNA (30)

Refinement Resolution (Å)

	0.5 - 1.0 (1)
	1.0 - 1.5 (20)
	1.5 - 2.0 (103)
	2.0 - 2.5 (91)
	2.5 - 3.0 (65)
	3.0 - 3.5 (28)
	3.5 - 4.0 (14)
	4.0 - 4.5 (6)
	> 4.5 (10)

Release Date

	2005 - 2009 (27)
	2010 - 2014 (67)
	2015 - 2019 (97)
	2020 - 2024 (139)
	2025 - 2029 (13)

Enzyme Classification Name

	Hydrolases (121)
	Transferases (59)
	Lyases (11)
	Oxidoreductases (10)
	Isomerases (4)
	Translocases (2)

Membrane Protein Annotation

	mpstruc (16)
	PDBTM (11)
	OPM (9)
	MemProtMD (8)

Symmetry Type

	Asymmetric (226)
	Cyclic (106)
	Dihedral (13)
	Icosahedral (2)
	Helical (1)

SCOP Classification

	Alpha and beta proteins (a/b) (41)
	Alpha and beta proteins (a+b) (23)
	Artifacts (25)
	All beta proteins (14)
	Multi-domain proteins (alpha and beta) (11)
	All alpha proteins (8)

AllSelected

1 to 25 of 343 Structures

Page 1 of 14

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2BVL \| pdb_00002bvl	Download File View File

Crystal structure of the catalytic domain of toxin B from Clostridium difficile in complex with UDP, Glc and manganese ion

Reinert, D.J., Jank, T., Aktories, K., Schulz, G.E.

(2005) J Mol Biology 351: 973

Released	2005-08-03
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Clostridioides difficile
Macromolecule	TOXIN B (protein)
Unique Ligands	GLC, MN, SO4, TBR, UDP

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2BVM \| pdb_00002bvm	Download File View File

Crystal structure of the catalytic domain of toxin B from Clostridium difficile in complex with UDP, Glc and manganese ion

Reinert, D.J., Jank, T., Aktories, K., Schulz, G.E.

(2005) J Mol Biology 351: 973

Released	2005-08-03
Method	X-RAY DIFFRACTION 2.55 Å
Organisms	Clostridioides difficile
Macromolecule	TOXIN B (protein)
Unique Ligands	GLC, MN, SO4, UDP

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2F6E \| pdb_00002f6e	Download File View File

Clostridium difficile Toxin A C-terminal fragment 1 (TcdA-f1)

Ng, K.K., Ho, J.G.

(2005) Proc Natl Acad Sci U S A 102: 18373-18378

Released	2005-12-20
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Clostridioides difficile
Macromolecule	Toxin A (protein)

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2G7C \| pdb_00002g7c	Download File View File

Clostridium difficile Toxin A Fragment Bound to aGal(1,3)bGal(1,4)bGlcNAc

Greco, A., Ho, J.G.S., Lin, S.J., Palcic, M.M., Rupnik, M., Ng, K.K.S.

(2006) Nat Struct Mol Biol 13: 460-461

Released	2006-04-18
Method	X-RAY DIFFRACTION 2 Å
Organisms	Clostridioides difficile
Macromolecule	Toxin A (protein)
Unique Ligands	GOL
Unique branched monosaccharides	GAL, GLA, NAG

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2L7K \| pdb_00002l7k	Download File View File

Solution NMR Structure of protein CD1104.2 from Clostridium difficile, Northeast Structural Genomics Consortium Target CfR130

Pulavarti, S.V.S.R.K., Eletsky, A., Mills, J.L., Sukumaran, D.K., Wang, H., Ciccosanti, C., Janjua, H., Acton, T.B., Xiao, R., Everett, J.K., Lee, H., Prestegard, J.H., Montelione, G.T., Szyperski, T., Northeast Structural Genomics Consortium (NESG)

To be published

Released	2011-02-02
Method	SOLUTION NMR
Organisms	Clostridioides difficile 630
Macromolecule	Uncharacterized protein (protein)

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2N6J \| pdb_00002n6j	Download File View File

Solution structure of Zmp1, a zinc-dependent metalloprotease secreted by Clostridium difficile

Banci, L., Cantini, F., Scarselli, M., Rubino, J.T., Martinelli, M.

(2016) J Biol Inorg Chem 21: 185-196

Released	2016-01-13
Method	SOLUTION NMR
Organisms	Clostridioides difficile 630
Macromolecule	Zinc metalloprotease Zmp1 (protein)
Unique Ligands	ZN

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2QJ6 \| pdb_00002qj6	Download File View File

Crystal structure analysis of a 14 repeat C-terminal fragment of toxin TcdA in Clostridium difficile

Albesa-Jove, D., Bertrand, T., Carpenter, L., Lim, J., Brown, K.A., Fairweather, N.

To be published

Released	2008-07-15
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Clostridioides difficile
Macromolecule	Toxin A (protein)

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2QZJ \| pdb_00002qzj	Download File View File

Crystal structure of a two-component response regulator from Clostridium difficile

Sugadev, R., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

To be published

Released	2007-09-04
Method	X-RAY DIFFRACTION 2.89 Å
Organisms	Clostridioides difficile 630
Macromolecule	Two-component response regulator (protein)

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2WN4 \| pdb_00002wn4	Download File View File

Structural Basis for Substrate Recognition in the Enzymatic Component of ADP-ribosyltransferase Toxin CDTa from Clostridium difficile

Sundriyal, A., Roberts, A.K., Shone, C.C., Acharya, K.R.

(2009) J Biological Chem 284: 28713

Released	2009-08-18
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Clostridioides difficile
Macromolecule	ADP-RIBOSYLTRANSFERASE ENZYMATIC COMPONENT (protein)

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2WN5 \| pdb_00002wn5	Download File View File

Structural Basis for Substrate Recognition in the Enzymatic Component of ADP-ribosyltransferase Toxin CDTa from Clostridium difficile

Sundriyal, A., Roberts, A.K., Shone, C.C., Acharya, K.R.

(2009) J Biological Chem 284: 28713

Released	2009-08-18
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Clostridioides difficile
Macromolecule	ADP-RIBOSYLTRANSFERASE ENZYMATIC COMPONENT (protein)

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2WN6 \| pdb_00002wn6	Download File View File

Structural Basis for Substrate Recognition in the Enzymatic Component of ADP-ribosyltransferase Toxin CDTa from Clostridium difficile

Sundriyal, A., Roberts, A.K., Shone, C.C., Acharya, K.R.

(2009) J Biological Chem 284: 28713

Released	2009-08-18
Method	X-RAY DIFFRACTION 1.96 Å
Organisms	Clostridioides difficile
Macromolecule	ADP-RIBOSYLTRANSFERASE ENZYMATIC COMPONENT (protein)
Unique Ligands	GOL, NDP

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2WN7 \| pdb_00002wn7	Download File View File

Structural Basis for Substrate Recognition in the Enzymatic Component of ADP-ribosyltransferase Toxin CDTa from Clostridium difficile

Sundriyal, A., Roberts, A.K., Shone, C.C., Acharya, K.R.

(2009) J Biological Chem 284: 28713

Released	2009-08-18
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Clostridioides difficile
Macromolecule	ADP-RIBOSYLTRANSFERASE ENZYMATIC COMPONENT (protein)
Unique Ligands	GOL, NAD

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2WN8 \| pdb_00002wn8	Download File View File

Structural Basis for Substrate Recognition in the Enzymatic Component of ADP-ribosyltransferase Toxin CDTa from Clostridium difficile

Sundriyal, A., Roberts, A.K., Shone, C.C., Acharya, K.R.

(2009) J Biological Chem 284: 28713

Released	2009-08-18
Method	X-RAY DIFFRACTION 2 Å
Organisms	Clostridioides difficile
Macromolecule	ADP-RIBOSYLTRANSFERASE ENZYMATIC COMPONENT (protein)

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3CVZ \| pdb_00003cvz	Download File View File

Structural insights into the molecular organization of the S-layer from Clostridium difficile

Albesa-Jove, D., Fagan, R.

(2009) Mol Microbiol 71: 1308-1322

Released	2009-03-17
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Clostridioides difficile
Macromolecule	S-layer protein (protein)
Unique Ligands	GLY, PO4

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3DSB \| pdb_00003dsb	Download File View File

The crystal structure of a possible acetyltransferase from Clostridium difficile 630

Tan, K., Shackelford, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published

Released	2008-09-09
Method	X-RAY DIFFRACTION 1.48 Å
Organisms	Clostridioides difficile 630
Macromolecule	Putative acetyltransferase (protein)
Unique Ligands	BET, SO4

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3EO8 \| pdb_00003eo8	Download File View File

Crystal structure of BluB-like flavoprotein (YP_001089088.1) from CLOSTRIDIUM DIFFICILE 630 at 1.74 A resolution

Joint Center for Structural Genomics (JCSG)

To be published

Released	2008-11-04
Method	X-RAY DIFFRACTION 1.74 Å
Organisms	Clostridioides difficile 630
Macromolecule	BluB-like flavoprotein (protein)
Unique Ligands	ACT, CL, FMN, GOL

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3FES \| pdb_00003fes	Download File View File

Crystal Structure of the ATP-dependent Clp Protease ClpC from Clostridium difficile

Kim, Y., Tesar, C., Li, H., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published

Released	2008-12-16
Method	X-RAY DIFFRACTION 1.82 Å
Organisms	Clostridioides difficile 630
Macromolecule	ATP-dependent Clp endopeptidase (protein)
Unique Ligands	EPE, MG, PG4

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3FZQ \| pdb_00003fzq	Download File View File

Crystal structure of putative haloacid dehalogenase-like hydrolase (YP_001086940.1) from Clostridium difficile 630 at 2.10 A resolution

Joint Center for Structural Genomics (JCSG)

To be published

Released	2009-02-10
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Clostridioides difficile 630
Macromolecule	Putative hydrolase (protein)
Unique Ligands	EDO, NA, PO4

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3G13 \| pdb_00003g13	Download File View File

Crystal structure of putative conjugative transposon recombinase from Clostridium difficile

Bagaria, A., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

To be published

Released	2009-02-10
Method	X-RAY DIFFRACTION 2 Å
Organisms	Clostridioides difficile 630
Macromolecule	Putative conjugative transposon recombinase (protein)
Unique Ligands	GOL, NA

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3G5J \| pdb_00003g5j	Download File View File

Crystal structure of N-terminal domain of putative ATP/GTP binding protein from Clostridium difficile 630

Nocek, B., Bigelow, L., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published

Released	2009-03-10
Method	X-RAY DIFFRACTION 1.76 Å
Organisms	Clostridioides difficile 630
Macromolecule	Putative ATP/GTP binding protein (protein)
Unique Ligands	GOL, PGE

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3G68 \| pdb_00003g68	Download File View File

CRYSTAL STRUCTURE OF A PUTATIVE PHOSPHOSUGAR ISOMERASE (CD3275) FROM CLOSTRIDIUM DIFFICILE 630 AT 1.80 A RESOLUTION

Joint Center for Structural Genomics (JCSG)

To be published

Released	2009-02-24
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Clostridioides difficile 630
Macromolecule	Putative phosphosugar isomerase (protein)
Unique Ligands	CIT, EDO

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3GFA \| pdb_00003gfa	Download File View File

Crystal structure of a putative nitroreductase in complex with fmn (cd3205) from clostridium difficile 630 at 1.35 A resolution

Joint Center for Structural Genomics (JCSG)

To be published

Released	2009-03-17
Method	X-RAY DIFFRACTION 1.35 Å
Organisms	Clostridioides difficile 630
Macromolecule	Putative nitroreductase (protein)
Unique Ligands	CL, FMN, GOL, MPD, MRD

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3H4O \| pdb_00003h4o	Download File View File

Crystal structure of a nitroreductase family protein (cd3355) from clostridium difficile 630 at 1.50 A resolution

Joint Center for Structural Genomics (JCSG)

To be published

Released	2009-05-19
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Clostridioides difficile 630
Macromolecule	NITROREDUCTASE FAMILY PROTEIN (protein)
Unique Ligands	FMN, MPD, MRD

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3HO6 \| pdb_00003ho6	Download File View File

Structure-function analysis of inositol hexakisphosphate-induced autoprocessing in clostridium difficile toxin A

Pruitt, R.N., Lacy, D.B.

(2009) J Biological Chem 284: 21934-21940

Released	2009-06-23
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Clostridioides difficile
Macromolecule	Toxin A (protein)
Unique Ligands	IHP

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3IPJ \| pdb_00003ipj	Download File View File

The crystal structure of one domain of the PTS system, IIabc component from Clostridium difficile

Zhang, R., Bigelow, L., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published

Released	2009-10-20
Method	X-RAY DIFFRACTION 1.2 Å
Organisms	Clostridioides difficile 630
Macromolecule	PTS system, IIabc component (protein)
Unique Ligands	ZN

1 to 25 of 343 Structures

Page 1 of 14

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Membrane Protein Annotation

Symmetry Type

SCOP Classification

2BVL | pdb_00002bvl

2BVM | pdb_00002bvm

2F6E | pdb_00002f6e

2G7C | pdb_00002g7c

2L7K | pdb_00002l7k

2N6J | pdb_00002n6j

2QJ6 | pdb_00002qj6

2QZJ | pdb_00002qzj

2WN4 | pdb_00002wn4

2WN5 | pdb_00002wn5

2WN6 | pdb_00002wn6

2WN7 | pdb_00002wn7

2WN8 | pdb_00002wn8

3CVZ | pdb_00003cvz

3DSB | pdb_00003dsb

3EO8 | pdb_00003eo8

3FES | pdb_00003fes

3FZQ | pdb_00003fzq

3G13 | pdb_00003g13

3G5J | pdb_00003g5j

3G68 | pdb_00003g68

3GFA | pdb_00003gfa

3H4O | pdb_00003h4o

3HO6 | pdb_00003ho6

3IPJ | pdb_00003ipj