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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Tagami, T."

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Search Summary

This query matches 31 Structures.

Refinements

Structure Determination Methodology

experimental (31)

Scientific Name of Source Organism

	Kribbella flavida DSM 17836 (13)
	Beta vulgaris (6)
	Cecembia lonarensis LW9 (3)
	uncultured bacterium (3)
	Arthrobacter globiformis (2)
	Aspergillus niger (1)
	Bacteroides thetaiotaomicron VPI-5482 (1)
	Lacticaseibacillus casei (1)
	Microdochium nivale (1)

Taxonomy

	Bacteria (23)
	Eukaryota (8)

Experimental Method

X-RAY DIFFRACTION (31)

Polymer Entity Type

Protein (31)

Refinement Resolution (Å)

	1.0 - 1.5 (6)
	1.5 - 2.0 (14)
	2.0 - 2.5 (6)
	2.5 - 3.0 (5)

Release Date

	2010 - 2014 (6)
	2015 - 2019 (10)
	2020 - 2024 (15)

Enzyme Classification Name

Hydrolases (25)

Symmetry Type

	Asymmetric (23)
	Cyclic (5)
	Dihedral (3)

SCOP Classification

	All beta proteins (6)
	Alpha and beta proteins (a/b) (6)

AllSelected

1 to 25 of 31 Structures

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Explore in 3D

3W37 \| pdb_00003w37	Download File View File

Sugar beet alpha-glucosidase with acarbose

Tagami, T., Yamashita, K., Okuyama, M., Mori, H., Yao, M., Kimura, A.

(2013) J Biological Chem 288: 19296-19303

Released	2013-05-29
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Beta vulgaris
Macromolecule	Alpha-glucosidase (protein)
Unique Ligands	ACY, GOL, NAG, SO4
Unique branched monosaccharides	AC1, FUC, GLC, NAG

Explore in 3D

3W38 \| pdb_00003w38	Download File View File

Sugar beet alpha-glucosidase

Tagami, T., Yamashita, K., Okuyama, M., Mori, H., Yao, M., Kimura, A.

(2013) J Biological Chem 288: 19296-19303

Released	2013-05-29
Method	X-RAY DIFFRACTION 2.79 Å
Organisms	Beta vulgaris
Macromolecule	Alpha-glucosidase (protein)
Unique Ligands	NAG, SO4
Unique branched monosaccharides	FUC, NAG

Explore in 3D

3WEL \| pdb_00003wel	Download File View File

Sugar beet alpha-glucosidase with acarviosyl-maltotriose

Tagami, T., Yamashita, K., Okuyama, M., Mori, H., Yao, M., Kimura, A.

(2014) J Biological Chem 290: 1796-1803

Released	2014-07-16
Method	X-RAY DIFFRACTION 1.84 Å
Organisms	Beta vulgaris
Macromolecule	Alpha-glucosidase (protein)
Unique Ligands	GOL, SO4
Unique branched monosaccharides	AC1, FUC, GLC, NAG

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3WEM \| pdb_00003wem	Download File View File

Sugar beet alpha-glucosidase with acarviosyl-maltotetraose

Tagami, T., Yamashita, K., Okuyama, M., Mori, H., Yao, M., Kimura, A.

(2014) J Biological Chem 290: 1796-1803

Released	2014-07-16
Method	X-RAY DIFFRACTION 2.591 Å
Organisms	Beta vulgaris
Macromolecule	Alpha-glucosidase (protein)
Unique Ligands	NAG, SO4
Unique branched monosaccharides	AC1, FUC, GLC, NAG

Explore in 3D

3WEN \| pdb_00003wen	Download File View File

Sugar beet alpha-glucosidase with acarviosyl-maltopentaose

Tagami, T., Yamashita, K., Okuyama, M., Mori, H., Yao, M., Kimura, A.

(2014) J Biological Chem 290: 1796-1803

Released	2014-07-16
Method	X-RAY DIFFRACTION 2.59 Å
Organisms	Beta vulgaris
Macromolecule	Alpha-glucosidase (protein)
Unique Ligands	NAG, SO4
Unique branched monosaccharides	AC1, FUC, GLC, NAG

Explore in 3D

3WEO \| pdb_00003weo	Download File View File

Sugar beet alpha-glucosidase with acarviosyl-maltohexaose

Tagami, T., Yamashita, K., Okuyama, M., Mori, H., Yao, M., Kimura, A.

(2014) J Biological Chem 290: 1796-1803

Released	2014-07-16
Method	X-RAY DIFFRACTION 1.45 Å
Organisms	Beta vulgaris
Macromolecule	Alpha-glucosidase (protein)
Unique Ligands	GOL, NAG, SO4
Unique branched monosaccharides	AC1, FUC, GLC, NAG

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5E1Q \| pdb_00005e1q	Download File View File

Mutant (D415G) GH97 alpha-galactosidase in complex with Gal-Lac

Matsunaga, K., Yamashita, K., Tagami, T., Yao, M., Okuyama, M., Kimura, A.

(2017) FEBS J 284: 766-783

Released	2016-10-05
Method	X-RAY DIFFRACTION 1.943 Å
Organisms	Bacteroides thetaiotaomicron VPI-5482
Macromolecule	Retaining alpha-galactosidase (protein)
Unique Ligands	CA, GOL
Unique branched monosaccharides	BGC, GAL, GLA

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5X3I \| pdb_00005x3i	Download File View File

Kfla1895 D451A mutant

Tanaka, Y., Chen, M., Tagami, T., Yao, M., Kimura, A.

To be published

Released	2018-02-07
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Kribbella flavida DSM 17836
Macromolecule	Glycoside hydrolase family 31 (protein)
Unique Ligands	GOL, SO4

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5X3J \| pdb_00005x3j	Download File View File

Kfla1895 D451A mutant in complex with cyclobis-(1->6)-alpha-nigerosyl

Tanaka, Y., Chen, M., Tagami, T., Yao, M., Kimura, A.

To be published

Released	2018-02-07
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Kribbella flavida DSM 17836
Macromolecule	Glycoside hydrolase family 31 (protein)
Unique Ligands	GOL, SO4
Unique branched monosaccharides	GLC

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5X3K \| pdb_00005x3k	Download File View File

Kfla1895 D451A mutant in complex with isomaltose

Tanaka, Y., Chen, M., Tagami, T., Yao, M., Kimura, A.

To be published

Released	2018-02-07
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Kribbella flavida DSM 17836
Macromolecule	Glycoside hydrolase family 31 (protein)
Unique Ligands	GOL, SO4
Unique branched monosaccharides	BGC, GLC

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5Z3A \| pdb_00005z3a	Download File View File

Glycosidase Wild Type

Tanaka, Y., Chen, M., Tagami, T., Yao, M., Kimura, A.

(2022) FEBS J 289: 1118-1134

Released	2019-05-15
Method	X-RAY DIFFRACTION 1.401 Å
Organisms	Kribbella flavida DSM 17836
Macromolecule	Glycoside hydrolase 15-related protein (protein)
Unique Ligands	CIT, GOL

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5Z3B \| pdb_00005z3b	Download File View File

Glycosidase Y48F

Tanaka, Y., Chen, M., Tagami, T., Yao, M., Kimura, A.

(2022) FEBS J 289: 1118-1134

Released	2019-05-15
Method	X-RAY DIFFRACTION 1.25 Å
Organisms	Kribbella flavida DSM 17836
Macromolecule	Glycoside hydrolase 15-related protein (protein)
Unique Ligands	CIT, GOL

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5Z3C \| pdb_00005z3c	Download File View File

Glycosidase E178A

Tanaka, Y., Chen, M., Tagami, T., Yao, M., Kimura, A.

(2022) FEBS J 289: 1118-1134

Released	2019-05-15
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Kribbella flavida DSM 17836
Macromolecule	Glycoside hydrolase 15-related protein (protein)
Unique Ligands	GOL

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5Z3D \| pdb_00005z3d	Download File View File

Glycosidase F290Y

Tanaka, Y., Chen, M., Tagami, T., Yao, M., Kimura, A.

(2022) FEBS J 289: 1118-1134

Released	2019-05-15
Method	X-RAY DIFFRACTION 1.25 Å
Organisms	Kribbella flavida DSM 17836
Macromolecule	Glycoside hydrolase 15-related protein (protein)
Unique Ligands	CIT, GOL

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5Z3E \| pdb_00005z3e	Download File View File

Glycosidase E335A

Tanaka, Y., Chen, M., Tagami, T., Yao, M., Kimura, A.

(2022) FEBS J 289: 1118-1134

Released	2019-05-15
Method	X-RAY DIFFRACTION 1.1 Å
Organisms	Kribbella flavida DSM 17836
Macromolecule	Glycoside hydrolase 15-related protein (protein)
Unique Ligands	CIT, GOL

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5Z3F \| pdb_00005z3f	Download File View File

Glycosidase E335A in complex with glucose

Tanaka, Y., Chen, M., Tagami, T., Yao, M., Kimura, A.

(2022) FEBS J 289: 1118-1134

Released	2019-05-15
Method	X-RAY DIFFRACTION 1.1 Å
Organisms	Kribbella flavida DSM 17836
Macromolecule	Glycoside hydrolase 15-related protein (protein)
Unique Ligands	BGC, CIT, GOL

Explore in 3D

7C24 \| pdb_00007c24	Download File View File

Glycosidase F290Y at pH8.0

Tagami, T., Kikuchi, A., Okuyama, M., Kimura, A.

(2022) FEBS J 289: 1118-1134

Released	2021-05-12
Method	X-RAY DIFFRACTION 1.71 Å
Organisms	Kribbella flavida DSM 17836
Macromolecule	Isomaltose glucohydrolase (protein)
Unique Ligands	GOL, NH4

Explore in 3D

7C25 \| pdb_00007c25	Download File View File

Glycosidase Wild Type at pH8.0

Tagami, T., Kikuchi, A., Okuyama, M., Kimura, A.

(2022) FEBS J 289: 1118-1134

Released	2021-05-12
Method	X-RAY DIFFRACTION 1.505 Å
Organisms	Kribbella flavida DSM 17836
Macromolecule	Isomaltose glucohydrolase (protein)
Unique Ligands	CIT, GOL, NH4

Explore in 3D

7C26 \| pdb_00007c26	Download File View File

Glycosidase Wild Type at pH4.5

Tagami, T., Kikuchi, A., Okuyama, M., Kimura, A.

(2022) FEBS J 289: 1118-1134

Released	2021-05-12
Method	X-RAY DIFFRACTION 1.803 Å
Organisms	Kribbella flavida DSM 17836
Macromolecule	Isomaltose glucohydrolase (protein)
Unique Ligands	CIT, GOL, NH4

Explore in 3D

7C27 \| pdb_00007c27	Download File View File

Glycosidase F290Y at pH4.5

Tagami, T., Kikuchi, A., Okuyama, M., Kimura, A.

(2022) FEBS J 289: 1118-1134

Released	2021-05-12
Method	X-RAY DIFFRACTION 1.91 Å
Organisms	Kribbella flavida DSM 17836
Macromolecule	Isomaltose glucohydrolase (protein)
Unique Ligands	CIT, GOL, NH4

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7XSF \| pdb_00007xsf	Download File View File

Crystal structure of ClAgl29A

Shishiuchi, R., Kang, H., Tagami, T., Okuyama, M.

(2022) ACS Omega 7: 47411-47423

Released	2023-01-18
Method	X-RAY DIFFRACTION 2.006 Å
Organisms	Cecembia lonarensis LW9
Macromolecule	Alpha-L-fucosidase (protein)
Unique Ligands	GOL, NA, PEG

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7XSG \| pdb_00007xsg	Download File View File

Crystal structure of ClAgl29B

Shishiuchi, R., Kang, H., Tagami, T., Okuyama, M.

(2022) ACS Omega 7: 47411-47423

Released	2023-01-18
Method	X-RAY DIFFRACTION 1.609 Å
Organisms	Cecembia lonarensis LW9
Macromolecule	Alpha-L-fucosidase (protein)
Unique Ligands	CIT, GOL, NA, PEG

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7XSH \| pdb_00007xsh	Download File View File

Crystal structure of ClAgl29B bound with L-glucose

Shishiuchi, R., Kang, H., Tagami, T., Okuyama, M.

(2022) ACS Omega 7: 47411-47423

Released	2023-01-18
Method	X-RAY DIFFRACTION 1.708 Å
Organisms	Cecembia lonarensis LW9
Macromolecule	Alpha-L-fucosidase (protein)
Unique Ligands	CIT, GOL, NA, PEG, Z8T

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7XTJ \| pdb_00007xtj	Download File View File

Crystal structure of E88A mutant of GH3 beta-xylosidase from Aspergillus niger (AnBX)

Kaenying, W., Kongsaeree, P.T., Tagami, T.

(2023) Appl Microbiol Biotechnol 107: 2335-2349

Released	2023-03-15
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Aspergillus niger
Macromolecule	Xylan 1,4-beta-xylosidase (protein)
Unique Ligands	GOL, NAG
Unique branched monosaccharides	BMA, MAN, NAG

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8H25 \| pdb_00008h25	Download File View File

Lacticaseibacillus casei GH35 beta-galactosidase LBCZ_0230

Saburi, W., Ota, T., Kato, K., Tagami, T., Yamashita, K., Yao, M., Mori, H.

(2023) J Appl Glycosci (1999) 70: 43-52

Released	2023-08-16
Method	X-RAY DIFFRACTION 2.295 Å
Organisms	Lacticaseibacillus casei
Macromolecule	Beta-galactosidase (protein)
Unique Ligands	EPE, GOL, PEG

1 to 25 of 31 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

Symmetry Type

SCOP Classification

3W37 | pdb_00003w37

3W38 | pdb_00003w38

3WEL | pdb_00003wel

3WEM | pdb_00003wem

3WEN | pdb_00003wen

3WEO | pdb_00003weo

5E1Q | pdb_00005e1q

5X3I | pdb_00005x3i

5X3J | pdb_00005x3j

5X3K | pdb_00005x3k

5Z3A | pdb_00005z3a

5Z3B | pdb_00005z3b

5Z3C | pdb_00005z3c

5Z3D | pdb_00005z3d

5Z3E | pdb_00005z3e

5Z3F | pdb_00005z3f

7C24 | pdb_00007c24

7C25 | pdb_00007c25

7C26 | pdb_00007c26

7C27 | pdb_00007c27

7XSF | pdb_00007xsf

7XSG | pdb_00007xsg

7XSH | pdb_00007xsh

7XTJ | pdb_00007xtj

8H25 | pdb_00008h25