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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Codee, J.D.C."

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Search Summary

This query matches 133 Structures.

Refinements

Structure Determination Methodology

experimental (133)

Scientific Name of Source Organism

	Homo sapiens (26)
	Drosophila melanogaster (12)
	Cellvibrio japonicus Ueda107 (8)
	Listeria monocytogenes (7)
	Cellvibrio japonicus (6)
	Aspergillus oryzae (5)
	Bacteroides thetaiotaomicron VPI-5482 (5)
	Acidobacterium capsulatum (4)
	Acidobacterium capsulatum ATCC 51196 (4)
	Niallia circulans (4)

More...

Taxonomy

	Bacteria (72)
	Eukaryota (58)
	Duplodnaviria (3)

Experimental Method

	X-RAY DIFFRACTION (131)
	SOLUTION NMR (2)
	SOLUTION SCATTERING (1)

Polymer Entity Type

Protein (133)

Refinement Resolution (Å)

	0.5 - 1.0 (1)
	1.0 - 1.5 (24)
	1.5 - 2.0 (62)
	2.0 - 2.5 (33)
	2.5 - 3.0 (9)
	3.0 - 3.5 (2)

Release Date

	2010 - 2014 (2)
	2015 - 2019 (36)
	2020 - 2024 (93)
	2025 - 2029 (2)

Enzyme Classification Name

	Hydrolases (78)
	Transferases (18)

Membrane Protein Annotation

	mpstruc (1)
	OPM (1)

Symmetry Type

	Asymmetric (101)
	Cyclic (31)
	Dihedral (1)

SCOP Classification

	Alpha and beta proteins (a/b) (13)
	All beta proteins (11)
	Artifacts (2)

AllSelected

1 to 25 of 133 Structures

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4WSJ \| pdb_00004wsj	Download File View File

Crystal structure of a bacterial fucodiase in complex with 1-((1R,2R,3R,4R,5R,6R)-2,3,4-trihydroxy-5-methyl-7-azabicyclo[4.1.0]heptan-7-yl)ethan-1-one

Davies, G.J., Wright, D.W.

(2015) Chem Sci 6: 2782-false

Released	2014-11-05
Method	X-RAY DIFFRACTION 1.64 Å
Organisms	Bacteroides thetaiotaomicron VPI-5482
Macromolecule	Alpha-L-fucosidase (protein)
Unique Ligands	3U3, SO4

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4WSK \| pdb_00004wsk	Download File View File

Crystal structure of a bacterial fucosidase with phenyl((1R,2R,3R,4R,5R,6R)-2,3,4-trihydroxy-5-methyl-7-azabicyclo[4.1.0]heptan-7-yl)methanone

Davies, G.J.

(2015) Chem Sci 6: 2782-false

Released	2014-11-12
Method	X-RAY DIFFRACTION 1.92 Å
Organisms	Bacteroides thetaiotaomicron VPI-5482
Macromolecule	Alpha-L-fucosidase (protein)
Unique Ligands	3U2, IMD, SO4

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5G0Q \| pdb_00005g0q	Download File View File

beta-glucuronidase with an activity-based probe (N-alkyl cyclophellitol aziridine) bound

Jin, Y., Wu, L., Jiang, J.B., Overkleeft, H.S., Davies, G.J.

(2017) Nat Chem Biol 13: 867-873

Released	2017-04-12
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Acidobacterium capsulatum
Macromolecule	BETA-GLUCURONIDASE (protein)
Unique Ligands	GOL, IF6

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5JAW \| pdb_00005jaw	Download File View File

Structure of a beta galactosidase with inhibitor

Offen, W., Davies, G.

(2017) Chem Commun (Camb) 53: 12528-12531

Released	2017-05-10
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Cellvibrio japonicus Ueda107
Macromolecule	Beta-galactosidase, putative, bgl35A (protein)
Unique Ligands	ACT, NA, UUU

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5L77 \| pdb_00005l77	Download File View File

A glycoside hydrolase mutant with an unreacted activity based probe bound

Jin, Y., Wu, L., Jiang, J.B., Overkleeft, H.S., Davies, G.J.

(2017) Nat Chem Biol 13: 867-873

Released	2017-05-31
Method	X-RAY DIFFRACTION 1.24 Å
Organisms	Acidobacterium capsulatum
Macromolecule	beta-glucuronidase (protein)
Unique Ligands	CL, GOL, GUX, PO4

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5L9Y \| pdb_00005l9y	Download File View File

Crystal structure of human heparanase, in complex with glucuronic acid configured aziridine probe JJB355

Wu, L., Jin, Y., Davies, G.J.

(2017) Nat Chem Biol 13: 867-873

Released	2017-05-31
Method	X-RAY DIFFRACTION 1.88 Å
Organisms	Homo sapiens
Macromolecule	Heparanase (protein)
Unique Ligands	6S6, EDO, NAG
Unique branched monosaccharides	FUC, NAG

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5L9Z \| pdb_00005l9z	Download File View File

Crystal structure of human heparanase nucleophile mutant (E343Q), in complex with unreacted glucuronic acid configured aziridine probe JJB355

Wu, L., Jin, Y., Davies, G.J.

(2017) Nat Chem Biol 13: 867-873

Released	2017-05-31
Method	X-RAY DIFFRACTION 1.57 Å
Organisms	Homo sapiens
Macromolecule	Heparanase (protein)
Unique Ligands	CL, EDO, GUX, NAG

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5LA4 \| pdb_00005la4	Download File View File

Crystal structure of apo human proheparanase

Wu, L., Jin, Y., Davies, G.J.

(2017) Nat Chem Biol 13: 867-873

Released	2017-05-31
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	Heparanase (protein)
Unique Ligands	EDO, NAG
Unique branched monosaccharides	BMA, FUC, NAG

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5LA7 \| pdb_00005la7	Download File View File

Crystal structure of human proheparanase, in complex with glucuronic acid configured aziridine probe JJB355

Wu, L., Jin, Y., Davies, G.J.

(2017) Nat Chem Biol 13: 867-873

Released	2017-05-31
Method	X-RAY DIFFRACTION 1.94 Å
Organisms	Homo sapiens
Macromolecule	Heparanase (protein)
Unique Ligands	6S6, EDO, NAG
Unique branched monosaccharides	FUC, NAG

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5MEH \| pdb_00005meh	Download File View File

Crystal structure of alpha-1,2-mannosidase from Caulobacter K31 strain in complex with 1-deoxymannojirimycin

Males, A., Davies, G.J.

(2017) Chembiochem 18: 1297-1304

Released	2016-12-21
Method	X-RAY DIFFRACTION 0.95 Å
Organisms	Caulobacter sp. K31
Macromolecule	Mannosyl-oligosaccharide 1,2-alpha-mannosidase (protein)
Unique Ligands	ACT, CA, DMJ, GOL, NA

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5N6S \| pdb_00005n6s	Download File View File

Thermotoga maritima family 1 Glycoside hydrolase complexed with Carba-Cyclophellitol transition state mimic

Offen, W., Davies, G.

(2017) J Am Chem Soc 139: 6534-6537

Released	2017-03-01
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Thermotoga maritima
Macromolecule	Beta-glucosidase A (protein)
Unique Ligands	8P5, ACT, CL, EDO, IMD, PEG, PGE

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5N6T \| pdb_00005n6t	Download File View File

Thermotoga maritima family 1 glycoside hydrolase complexed with a cyclophellitol analogue transition state mimic

Offen, W., Davies, G.

(2017) J Am Chem Soc 139: 6534-6537

Released	2017-03-01
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Thermotoga maritima
Macromolecule	Beta-glucosidase A (protein)
Unique Ligands	8P2, CL, EDO

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5NPB \| pdb_00005npb	Download File View File

Crystal Structure of cjAgd31B (alpha-transglucosylase from Glycoside Hydrolase Family 31) in complex with alpha Cyclophellitol Cyclosulfate probe ME647

Wu, L., Davies, G.J.

(2017) ACS Cent Sci 3: 784-793

Released	2017-08-09
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Cellvibrio japonicus
Macromolecule	Oligosaccharide 4-alpha-D-glucosyltransferase (protein)
Unique Ligands	93Z, OXL, PG4, SO4

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5NPC \| pdb_00005npc	Download File View File

Crystal Structure of D412N nucleophile mutant cjAgd31B (alpha-transglucosylase from Glycoside Hydrolase Family 31) in complex with unreacted alpha Cyclophellitol Cyclosulfate probe ME647

Wu, L., Davies, G.J.

(2017) ACS Cent Sci 3: 784-793

Released	2017-08-09
Method	X-RAY DIFFRACTION 1.96 Å
Organisms	Cellvibrio japonicus
Macromolecule	Oligosaccharide 4-alpha-D-glucosyltransferase (protein)
Unique Ligands	94E, EDO, OXL, PG4, SO4

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5NPD \| pdb_00005npd	Download File View File

Crystal Structure of D412N nucleophile mutant cjAgd31B (alpha-transglucosylase from Glycoside Hydrolase Family 31) in complex with alpha Cyclophellitol Aziridine probe CF021

Wu, L., Davies, G.J.

(2017) ACS Cent Sci 3: 784-793

Released	2017-08-09
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Cellvibrio japonicus
Macromolecule	Oligosaccharide 4-alpha-D-glucosyltransferase (protein)
Unique Ligands	94B, EDO, OXL, PG4, SO4

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5NPE \| pdb_00005npe	Download File View File

Crystal Structure of cjAgd31B (alpha-transglucosylase from Glycoside Hydrolase Family 31) in complex with beta Cyclophellitol Aziridine probe KY358

Wu, L., Davies, G.J.

(2017) ACS Cent Sci 3: 784-793

Released	2017-08-09
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Cellvibrio japonicus Ueda107
Macromolecule	Oligosaccharide 4-alpha-D-glucosyltransferase (protein)
Unique Ligands	948, EDO, OXL, PG4, SO4

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5NPF \| pdb_00005npf	Download File View File

Crystal structure of txGH116 (beta-glucosidase from Thermoanaerobacterium xylolyticum) in complex with beta Cyclophellitol Cyclosulfate probe ME594

Wu, L., Offen, W.A., Breen, I.Z., Davies, G.J.

(2017) ACS Cent Sci 3: 784-793

Released	2017-08-09
Method	X-RAY DIFFRACTION 1.38 Å
Organisms	Thermoanaerobacterium xylanolyticum
Macromolecule	Glucosylceramidase (protein)
Unique Ligands	945, CA, EDO

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5O0S \| pdb_00005o0s	Download File View File

Crystal structure of txGH116 (beta-glucosidase from Thermoanaerobacterium xylolyticum) in complex with unreacted beta Cyclophellitol Cyclosulfate probe ME711

Wu, L., Offen, W.A., Breen, I.Z., Davies, G.J.

(2017) ACS Cent Sci 3: 784-793

Released	2017-08-09
Method	X-RAY DIFFRACTION 1.16 Å
Organisms	Thermoanaerobacterium xylanolyticum LX-11
Macromolecule	Glucosylceramidase (protein)
Unique Ligands	9FQ, CA, EDO

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5OSS \| pdb_00005oss	Download File View File

Beta-glucosidase from Thermotoga maritima in complex with Gluco-1H-imidazole

Offen, W.A., Schroeder, S.P., Davies, G.J., Overkleeft, H.S.

(2018) J Am Chem Soc 140: 5045-5048

Released	2018-04-11
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Thermotoga maritima MSB8
Macromolecule	Beta-glucosidase A (protein)
Unique Ligands	AEZ, CL, EDO, NA

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5OST \| pdb_00005ost	Download File View File

Beta-glucosidase from Thermoanaerobacterium xylolyticum GH116 in complex with Gluco-1H-imidazole

Davies, G.J., Offen, W.A.

(2018) J Am Chem Soc 140: 5045-5048

Released	2018-04-11
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Thermoanaerobacterium xylanolyticum LX-11
Macromolecule	Glucosylceramidase (protein)
Unique Ligands	AEZ, CA, CL, EDO

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6CZT \| pdb_00006czt	Download File View File

CS-rosetta determined structures of the N-terminal domain of AlgF from P. aeruginosa

Tammam, S., Howell, P.L.

To be published

Released	2019-04-17
Method	SOLUTION NMR
Organisms	Pseudomonas aeruginosa PAO1
Macromolecule	Alginate biosynthesis protein AlgF (protein)

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6D10 \| pdb_00006d10	Download File View File

CS-rosetta determined structures of the C-terminal domain of AlgF from P. aeruginosa

Tammam, S., Howell, P.L.

To be published

Released	2019-04-17
Method	SOLUTION NMR SOLUTION SCATTERING
Organisms	Pseudomonas aeruginosa PAO1
Macromolecule	Alginate biosynthesis protein AlgF (protein)

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6I6R \| pdb_00006i6r	Download File View File

New Irreversible a-l-Iduronidase Inhibitors and Activity-Based Probes

Gloster, T.M., McMahon, S.A., Oehler, V.

(2018) Chemistry 24: 19081-19088

Released	2018-12-05
Method	X-RAY DIFFRACTION 2.02 Å
Organisms	Homo sapiens
Macromolecule	Alpha-L-iduronidase (protein)
Unique Ligands	CL, GOL, H62, NAG, TLA
Unique branched monosaccharides	BMA, NAG

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6I6X \| pdb_00006i6x	Download File View File

New Irreversible a-l-Iduronidase Inhibitors and Activity-Based Probes

Gloster, T.M., McMahon, S.A., Oehler, V.

(2018) Chemistry 24: 19081-19088

Released	2018-12-05
Method	X-RAY DIFFRACTION 2.39 Å
Organisms	Homo sapiens
Macromolecule	Alpha-L-iduronidase (protein)
Unique Ligands	CL, GOL, H6B, NAG, TLA
Unique branched monosaccharides	BMA, MAN, NAG

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6IBK \| pdb_00006ibk	Download File View File

Crystal structure of human alpha-galactosidase A in complex with alpha-galactose configured cyclosulfamidate ME763

Rowland, R.J., Wu, L., Davies, G.J.

(2019) Chem Sci

Released	2019-10-09
Method	X-RAY DIFFRACTION 1.99 Å
Organisms	Homo sapiens
Macromolecule	Alpha-galactosidase A (protein)
Unique Ligands	ACT, EDO, NAG, PEG, SO4, YTW
Unique branched monosaccharides	BMA, MAN, NAG

1 to 25 of 133 Structures

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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

4WSJ | pdb_00004wsj

4WSK | pdb_00004wsk

5G0Q | pdb_00005g0q

5JAW | pdb_00005jaw

5L77 | pdb_00005l77

5L9Y | pdb_00005l9y

5L9Z | pdb_00005l9z

5LA4 | pdb_00005la4

5LA7 | pdb_00005la7

5MEH | pdb_00005meh

5N6S | pdb_00005n6s

5N6T | pdb_00005n6t

5NPB | pdb_00005npb

5NPC | pdb_00005npc

5NPD | pdb_00005npd

5NPE | pdb_00005npe

5NPF | pdb_00005npf

5O0S | pdb_00005o0s

5OSS | pdb_00005oss

5OST | pdb_00005ost

6CZT | pdb_00006czt

6D10 | pdb_00006d10

6I6R | pdb_00006i6r

6I6X | pdb_00006i6x

6IBK | pdb_00006ibk