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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Holck, J."

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Search Summary

This query matches 20 Structures.

Refinements

Structure Determination Methodology

experimental (20)

Scientific Name of Source Organism

	uncultured bacterium (5)
	Bacteroides fragilis (2)
	Bacteroides ovatus (2)
	Tannerella forsythia (2)
	Treponema denticola ATCC 35405 (2)
	Trueperella pyogenes (2)
	Bacteroides cellulosilyticus (1)
	Flagellimonas eckloniae (1)
	Niabella aurantiaca (1)
	Niabella aurantiaca DSM 17617 (1)

More...

Taxonomy

Bacteria (20)

Experimental Method

X-RAY DIFFRACTION (20)

Polymer Entity Type

Protein (20)

Refinement Resolution (Å)

	1.0 - 1.5 (2)
	1.5 - 2.0 (7)
	2.0 - 2.5 (7)
	2.5 - 3.0 (4)

Release Date

	2015 - 2019 (3)
	2020 - 2024 (10)
	2025 - 2029 (7)

Enzyme Classification Name

Hydrolases (9)

Symmetry Type

	Asymmetric (13)
	Cyclic (5)
	Dihedral (2)

AllSelected

1 to 20 of 20 Structures

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6QPS \| pdb_00006qps	Download File View File

Structural characterization of a mannuronic acid specific polysaccharide family 6 lyase enzyme from human gut microbiota

Fredslund, F., Stender, E.G.P., Svensson, B., Welner, D.H.

(2019) J Biological Chem 294: 17915-17930

Released	2019-09-25
Method	X-RAY DIFFRACTION 1.287 Å
Organisms	Bacteroides cellulosilyticus
Macromolecule	Polysaccharide Lyase Family 6 (protein)
Unique Ligands	ACT, CA

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6RZN \| pdb_00006rzn	Download File View File

Crystal structure of the N-terminal carbohydrate binding module family 48 and ferulic acid esterase from the multi-enzyme CE1-GH62-GH10

Fredslund, F., Welner, D.H., Wilkens, C.

(2019) J Biological Chem 294: 17339-17353

Released	2019-09-25
Method	X-RAY DIFFRACTION 1.907 Å
Organisms	uncultured bacterium
Macromolecule	Ferulic acid esterase (protein)

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6RZO \| pdb_00006rzo	Download File View File

Crystal structure of the N-terminal carbohydrate binding module family 48 and ferulic acid esterase from the multi-enzyme CE1-GH62-GH10

Fredslund, F., Welner, D.H., Wilkens, C.

(2019) J Biological Chem 294: 17339-17353

Released	2019-09-25
Method	X-RAY DIFFRACTION 1.632 Å
Organisms	uncultured bacterium
Macromolecule	Ferulic acid esterase (protein)

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7AJ0 \| pdb_00007aj0	Download File View File

Crystal structure of PsFucS1 sulfatase from Pseudoalteromonas sp.

Roret, T., Mikkelsen, M.D., Czjzek, M., Meyer, A.S.

(2021) Sci Rep 11: 19523-19523

Released	2021-09-08
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Pseudoalteromonas sp. MB47
Macromolecule	Arylsulfatase (protein)
Unique Ligands	CA, CL

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8BDD \| pdb_00008bdd	Download File View File

Crystal structure of Bacteroides ovatus CP926 PL17 alginate lyase

Roenne, M.E., Tandrup, T., Wilkens, C.

(2023) Appl Environ Microbiol 89: e0118523-e0118523

Released	2023-08-30
Method	X-RAY DIFFRACTION 1.61 Å
Organisms	Bacteroides ovatus
Macromolecule	Alginate lyase family protein (protein)
Unique Ligands	NI

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8BDQ \| pdb_00008bdq	Download File View File

Crystal structure of Bacteroides ovatus CP926 PL38 alginate lyase

Roenne, M.E., Tandrup, T., Wilkens, C.

(2023) Appl Environ Microbiol 89: e0118523-e0118523

Released	2023-08-30
Method	X-RAY DIFFRACTION 2.11 Å
Organisms	Bacteroides ovatus
Macromolecule	Alginate lyase family protein (protein)
Unique Ligands	SO4

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8BPD \| pdb_00008bpd	Download File View File

Structural and Functional Characterization of the Novel Endo-alpha(1,4)-Fucoidanase Mef1 from the Marine Bacterium Muricauda eckloniae

Mikkelsen, M.D., Meyer, A.S., Morth, J.P.

(2023) Acta Crystallogr D Struct Biol 79: 1026-1043

Released	2023-11-08
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Flagellimonas eckloniae
Macromolecule	Glycosyl hydrolase (protein)
Unique Ligands	3CX, CA, EDO

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8P4L \| pdb_00008p4l	Download File View File

Beta-N-acetylgalactosaminidase from Niabella aurantiaca

Fjermedal, S., Wilkens, C.

(2024) FEBS J 291: 1439-1456

Released	2024-01-17
Method	X-RAY DIFFRACTION 2.79 Å
Organisms	Niabella aurantiaca
Macromolecule	Beta-N-acetylgalactosaminidase (protein)

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8Q8H \| pdb_00008q8h	Download File View File

Crystal Structure of Apo beta-D-GalNAcase from Niabella aurantiaca (Structure 2)

Morth, J.P., Moreno Prieto, E.S., Siebenhaar, S.

(2024) FEBS J 291: 1439-1456

Released	2024-05-15
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Niabella aurantiaca DSM 17617
Macromolecule	beta-D-GalNAcase from Niabella aurantiaca DSM 17617 (protein)
Unique Ligands	NA, SO4

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9EU1 \| pdb_00009eu1	Download File View File

GH29A alpha-L-fucosidase

Yang, Y.Y., Zeuner, B., Morth, J.P.

(2025) FEBS J 292: 653-680

Released	2025-03-05
Method	X-RAY DIFFRACTION 1.92 Å
Organisms	Bacteroides fragilis
Macromolecule	Alpha-L-fucosidase (protein)
Unique Ligands	BTB, CL, NA, SO4, TRS

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9EU2 \| pdb_00009eu2	Download File View File

GH29A alpha-L-fucosidase

Yang, Y.Y., Zeuner, B., Morth, J.P.

(2025) FEBS J 292: 653-680

Released	2025-03-05
Method	X-RAY DIFFRACTION 1.84 Å
Organisms	Tannerella forsythia
Macromolecule	Alpha-L-fucosidase (protein)
Unique Ligands	EDO, NA, ZN

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9EU3 \| pdb_00009eu3	Download File View File

GH29A alpha-L-fucosidase

Yang, Y.Y., Zeuner, B., Morth, J.P.

(2025) FEBS J 292: 653-680

Released	2025-03-05
Method	X-RAY DIFFRACTION 2.28 Å
Organisms	Tannerella forsythia
Macromolecule	Alpha-L-fucosidase (protein)
Unique Ligands	CL, FUL, ZN

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9EU4 \| pdb_00009eu4	Download File View File

GH29A alpha-L-fucosidase

Yang, Y.Y., Zeuner, B., Morth, J.P.

(2025) FEBS J 292: 653-680

Released	2025-03-05
Method	X-RAY DIFFRACTION 2.33 Å
Organisms	Bacteroides fragilis
Macromolecule	Exported alpha-L-fucosidase protein (protein)
Unique Ligands	FUL, SO4

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9FVF \| pdb_00009fvf	Download File View File

UMG-SP3 amidase from uncultured bacterium

Rotilio, L., Morth, J.P.

(2025) Angew Chem Int Ed Engl 64: e202419535-e202419535

Released	2025-02-05
Method	X-RAY DIFFRACTION 2.32 Å
Organisms	uncultured bacterium
Macromolecule	Amidase UMG-SP3 (protein)
Unique Ligands	PG6, SO4

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9FW1 \| pdb_00009fw1	Download File View File

UMG-SP3 amidase from uncultured bacterium in complex with PMSF

Rotilio, L., Morth, J.P.

(2025) Angew Chem Int Ed Engl 64: e202419535-e202419535

Released	2025-02-05
Method	X-RAY DIFFRACTION 2.18 Å
Organisms	uncultured bacterium
Macromolecule	UMG-SP3 amidase (protein)
Unique Ligands	PMS, SO4

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9FYL \| pdb_00009fyl	Download File View File

Lacto-N-biosidase from Treponema denticola ATCC 35405, HisTag bound in active site

Vuillemin, M., Siebenhaar, S., Zeuner, B., Morth, J.P.

(2025) Chembiochem 26: e202400710-e202400710

Released	2024-10-09
Method	X-RAY DIFFRACTION 2.24 Å
Organisms	Treponema denticola ATCC 35405
Macromolecule	Glycoside hydrolase family 20 catalytic domain-containing protein (protein)
Unique Ligands	ZN

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9FYM \| pdb_00009fym	Download File View File

Lacto-N-biosidase from Treponema denticola ATCC 35405

Vuillemin, M., Siebenhaar, S., Zeuner, B., Morth, J.P.

(2025) Chembiochem 26: e202400710-e202400710

Released	2024-10-09
Method	X-RAY DIFFRACTION 1.34 Å
Organisms	Treponema denticola ATCC 35405
Macromolecule	Glycoside hydrolase family 20 catalytic domain-containing protein (protein)
Unique Ligands	IMD, NA, ZN

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9FYN \| pdb_00009fyn	Download File View File

Lacto-N-biosidase from Trueperella pyogenes

Vuillemin, M., Siebenhaar, S., Zeuner, B., Morth, J.P.

(2025) Chembiochem 26: e202400710-e202400710

Released	2024-10-09
Method	X-RAY DIFFRACTION 1.79 Å
Organisms	Trueperella pyogenes
Macromolecule	lacto-n-biosidase GH20 (protein)
Unique Ligands	NI

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9FYO \| pdb_00009fyo	Download File View File

Lacto-N-biosidase from Trueperella pyogenes

Vuillemin, M., Siebenhaar, S., Zeuner, B., Morth, J.P.

(2025) Chembiochem 26: e202400710-e202400710

Released	2024-10-09
Method	X-RAY DIFFRACTION 2.77 Å
Organisms	Trueperella pyogenes
Macromolecule	TrpyGH20 (protein)
Unique Ligands	NI
Unique branched monosaccharides	GAL, NAG

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9FZ1 \| pdb_00009fz1	Download File View File

UMG-SP3 amidase from uncultured bacterium in complex with 4,4'-MDA

Rotilio, L., Morth, J.P.

(2025) Angew Chem Int Ed Engl 64: e202419535-e202419535

Released	2025-02-05
Method	X-RAY DIFFRACTION 2 Å
Organisms	uncultured bacterium
Macromolecule	UMG-SP3 (protein)
Unique Ligands	A1IHK, ACT

1 to 20 of 20 Structures

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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.

6QPS | pdb_00006qps

Structural characterization of a mannuronic acid specific polysaccharide family 6 lyase enzyme from human gut microbiota

6RZN | pdb_00006rzn

Crystal structure of the N-terminal carbohydrate binding module family 48 and ferulic acid esterase from the multi-enzyme CE1-GH62-GH10

6RZO | pdb_00006rzo

Crystal structure of the N-terminal carbohydrate binding module family 48 and ferulic acid esterase from the multi-enzyme CE1-GH62-GH10

7AJ0 | pdb_00007aj0

Crystal structure of PsFucS1 sulfatase from Pseudoalteromonas sp.

8BDD | pdb_00008bdd

Crystal structure of Bacteroides ovatus CP926 PL17 alginate lyase

8BDQ | pdb_00008bdq

Crystal structure of Bacteroides ovatus CP926 PL38 alginate lyase

8BPD | pdb_00008bpd

Structural and Functional Characterization of the Novel Endo-alpha(1,4)-Fucoidanase Mef1 from the Marine Bacterium Muricauda eckloniae

8P4L | pdb_00008p4l

Beta-N-acetylgalactosaminidase from Niabella aurantiaca

8Q8H | pdb_00008q8h

Crystal Structure of Apo beta-D-GalNAcase from Niabella aurantiaca (Structure 2)

9EU1 | pdb_00009eu1

GH29A alpha-L-fucosidase

9EU2 | pdb_00009eu2

GH29A alpha-L-fucosidase

9EU3 | pdb_00009eu3

GH29A alpha-L-fucosidase

9EU4 | pdb_00009eu4

GH29A alpha-L-fucosidase

9FVF | pdb_00009fvf

UMG-SP3 amidase from uncultured bacterium

9FW1 | pdb_00009fw1

UMG-SP3 amidase from uncultured bacterium in complex with PMSF

9FYL | pdb_00009fyl

Lacto-N-biosidase from Treponema denticola ATCC 35405, HisTag bound in active site

9FYM | pdb_00009fym

Lacto-N-biosidase from Treponema denticola ATCC 35405

9FYN | pdb_00009fyn

Lacto-N-biosidase from Trueperella pyogenes

9FYO | pdb_00009fyo

Lacto-N-biosidase from Trueperella pyogenes

9FZ1 | pdb_00009fz1

UMG-SP3 amidase from uncultured bacterium in complex with 4,4'-MDA

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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

Symmetry Type

6QPS | pdb_00006qps

6RZN | pdb_00006rzn

6RZO | pdb_00006rzo

7AJ0 | pdb_00007aj0

8BDD | pdb_00008bdd

8BDQ | pdb_00008bdq

8BPD | pdb_00008bpd

8P4L | pdb_00008p4l

8Q8H | pdb_00008q8h

9EU1 | pdb_00009eu1

9EU2 | pdb_00009eu2

9EU3 | pdb_00009eu3

9EU4 | pdb_00009eu4

9FVF | pdb_00009fvf

9FW1 | pdb_00009fw1

9FYL | pdb_00009fyl

9FYM | pdb_00009fym

9FYN | pdb_00009fyn

9FYO | pdb_00009fyo

9FZ1 | pdb_00009fz1