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234,785 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Fantin, V.R."

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Search Summary

This query matches 32 Structures.

Refinements

Structure Determination Methodology

experimental (32)

Scientific Name of Source Organism

	metagenomes (7)
	Thermus thermophilus HB8 (5)
	uncultured bacterium (4)
	Arthrobacter (3)
	Thermotoga maritima (3)
	Alphaproteobacteria bacterium (2)
	Bacillus subtilis (2)
	Geotrichum sp. M128 (2)
	Homo sapiens (2)
	Escherichia coli K-12 (1)

More...

Taxonomy

	Bacteria (21)
	unclassified sequences (7)
	Eukaryota (4)

Experimental Method

	X-RAY DIFFRACTION (31)
	SOLUTION NMR (1)

Polymer Entity Type

Protein (32)

Refinement Resolution (Å)

	1.0 - 1.5 (7)
	1.5 - 2.0 (12)
	2.0 - 2.5 (10)
	2.5 - 3.0 (1)
	3.0 - 3.5 (1)

Release Date

	1990 - 1994 (1)
	1995 - 1999 (5)
	2005 - 2009 (5)
	2010 - 2014 (13)
	2015 - 2019 (2)
	2020 - 2024 (4)
	2025 - 2029 (2)

Enzyme Classification Name

	Hydrolases (17)
	Oxidoreductases (7)

Symmetry Type

	Asymmetric (13)
	Cyclic (17)
	Dihedral (3)

SCOP Classification

	All beta proteins (5)
	Alpha and beta proteins (a/b) (6)
	Artifacts (1)

AllSelected

1 to 25 of 32 Structures

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1IDM \| pdb_00001idm	Download File View File

3-ISOPROPYLMALATE DEHYDROGENASE, LOOP-DELETED CHIMERA

Sakurai, M., Ohzeki, M., Moriyama, H., Sato, M., Tanaka, N.

(1996) Acta Crystallogr D Biol Crystallogr 52: 124-128

Released	1995-09-15
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Thermus thermophilus HB8
Macromolecule	3-ISOPROPYLMALATE DEHYDROGENASE (protein)

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1IPD \| pdb_00001ipd	Download File View File

THREE-DIMENSIONAL STRUCTURE OF A HIGHLY THERMOSTABLE ENZYME, 3-ISOPROPYLMALATE DEHYDROGENASE OF THERMUS THERMOPHILUS AT 2.2 ANGSTROMS RESOLUTION

Imada, K., Sato, M., Tanaka, N., Katsube, Y., Matsuura, Y., Oshima, T.

(1991) J Mol Biology 222: 725-738

Released	1993-10-31
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Thermus thermophilus
Macromolecule	3-ISOPROPYLMALATE DEHYDROGENASE (protein)
Unique Ligands	SO4

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1OSI \| pdb_00001osi	Download File View File

STRUCTURE OF 3-ISOPROPYLMALATE DEHYDROGENASE

Qu, C., Akanuma, S., Moriyama, H., Tanaka, N., Oshima, T.

(1997) Protein Eng 10: 45-52

Released	1997-01-27
Method	X-RAY DIFFRACTION 3 Å
Organisms	Thermus thermophilus HB8
Macromolecule	3-ISOPROPYLMALATE DEHYDROGENASE (protein)

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1OSJ \| pdb_00001osj	Download File View File

STRUCTURE OF 3-ISOPROPYLMALATE DEHYDROGENASE

Qu, C., Akanuma, S., Moriyama, H., Tanaka, N., Oshima, T.

(1997) Protein Eng 10: 45-52

Released	1997-01-27
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	Thermus thermophilus HB8
Macromolecule	3-ISOPROPYLMALATE DEHYDROGENASE (protein)

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1XAA \| pdb_00001xaa	Download File View File

3-ISOPROPYLMALATE DEHYDROGENASE, LOW TEMPERATURE (100K) STRUCTURE

Nagata, C., Moriyama, H., Tanaka, N.

(1996) Acta Crystallogr D Biol Crystallogr 52: 623-630

Released	1996-04-03
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Thermus thermophilus HB8
Macromolecule	3-ISOPROPYLMALATE DEHYDROGENASE (protein)

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1XAB \| pdb_00001xab	Download File View File

3-ISOPROPYLMALATE DEHYDROGENASE, LOW TEMPERATURE (150K) STRUCTURE

Nagata, C., Moriyama, H., Tanaka, N.

(1996) Acta Crystallogr D Biol Crystallogr 52: 623-630

Released	1996-04-03
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Thermus thermophilus HB8
Macromolecule	3-ISOPROPYLMALATE DEHYDROGENASE (protein)

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2DCY \| pdb_00002dcy	Download File View File

Crystal structure of Bacillus subtilis family-11 xylanase

Kondo, H., Miyazaki, K., Takenouchi, M., Noro, N., Suzuki, M., Tsuda, S.

(2006) J Biological Chem 281: 10236-10242

Released	2006-02-07
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Bacillus subtilis
Macromolecule	Endo-1,4-beta-xylanase A (protein)
Unique Ligands	DIO, TAR, TLA

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2DCZ \| pdb_00002dcz	Download File View File

Thermal Stabilization of Bacillus subtilis Family-11 Xylanase By Directed Evolution

Kondo, H., Miyazaki, K., Takenouchi, M., Noro, N., Suzuki, M., Tsuda, S.

(2006) J Biological Chem 281: 10236-10242

Released	2006-02-07
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Bacillus subtilis
Macromolecule	Endo-1,4-beta-xylanase A (protein)
Unique Ligands	DIO, SO4

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2EBS \| pdb_00002ebs	Download File View File

Crystal Structure Anaalysis of Oligoxyloglucan reducing-end-specific cellobiohydrolase (OXG-RCBH) D465N Mutant Complexed with a Xyloglucan Heptasaccharide

Yaoi, K., Kondo, H., Hiyoshi, A., Noro, N., Sugimoto, H., Miyazaki, K., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2007) J Mol Biology 370: 53-62

Released	2007-06-26
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Geotrichum sp. M128
Macromolecule	Oligoxyloglucan reducing end-specific cellobiohydrolase (protein)
Unique branched monosaccharides	BGC, XYS

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2ZWN \| pdb_00002zwn	Download File View File

Crystal structure of the novel two-domain type laccase from a metagenome

Komori, H., Miyazaki, K., Higuchi, Y.

(2009) FEBS Lett 583: 1189-1195

Released	2009-04-07
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	metagenomes
Macromolecule	two-domain type laccase (protein)
Unique Ligands	C2O, CL, CU

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3A0F \| pdb_00003a0f	Download File View File

The crystal structure of Geotrichum sp. M128 xyloglucanase

Yaoi, K., Kondo, H., Hiyoshi, A., Noro, N., Sugimoto, H., Tsuda, S., Miyazaki, K.

(2009) FEBS J 276: 5094-5100

Released	2009-09-08
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Geotrichum sp. M128
Macromolecule	Xyloglucanase (protein)

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3AYU \| pdb_00003ayu	Download File View File

Crystal structure of MMP-2 active site mutant in complex with APP-drived decapeptide inhibitor

Hashimoto, H., Takeuchi, T., Komatsu, K., Miyazaki, K., Sato, M., Higashi, S.

(2011) J Biological Chem

Released	2011-08-03
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	72 kDa type IV collagenase (protein) Amyloid beta A4 protein (protein)
Unique Ligands	CA, ZN

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3UG3 \| pdb_00003ug3	Download File View File

Crystal structure of alpha-L-arabinofuranosidase from Thermotoga maritima ligand free form

Im, D.-H., Miyazaki, K., Wakagi, T., Fushinobu, S.

(2012) Biosci Biotechnol Biochem 76: 423-428

Released	2012-03-07
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Thermotoga maritima
Macromolecule	Alpha-L-arabinofuranosidase (protein)
Unique Ligands	EDO, NA, TRS

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3UG4 \| pdb_00003ug4	Download File View File

Crystal structure of alpha-L-arabinofuranosidase from Thermotoga maritima arabinose complex

Im, D.-H., Miyazaki, K., Wakagi, T., Fushinobu, S.

(2012) Biosci Biotechnol Biochem 76: 423-428

Released	2012-03-07
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Thermotoga maritima
Macromolecule	Alpha-L-arabinofuranosidase (protein)
Unique Ligands	AHR, TRS

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3UG5 \| pdb_00003ug5	Download File View File

Crystal structure of alpha-L-arabinofuranosidase from Thermotoga maritima xylose complex

Im, D.-H., Miyazaki, K., Wakagi, T., Fushinobu, S.

(2012) Biosci Biotechnol Biochem 76: 423-428

Released	2012-03-07
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Thermotoga maritima
Macromolecule	Alpha-L-arabinofuranosidase (protein)
Unique Ligands	TRS, XYP

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3WH5 \| pdb_00003wh5	Download File View File

Crystal structure of GH1 beta-glucosidase Td2F2

Jo, T., Fushinobu, S., Uchiyama, T., Yaoi, K.

(2016) FEBS J 283: 2340-2353

Released	2014-09-03
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	metagenomes
Macromolecule	beta-glucosidase (protein)
Unique Ligands	GOL, NA, NHE

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3WH6 \| pdb_00003wh6	Download File View File

Crystal structure of GH1 beta-glucosidase Td2F2 glucose complex

Jo, T., Fushinobu, S., Uchiyama, T., Yaoi, K.

(2016) FEBS J 283: 2340-2353

Released	2014-09-03
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	metagenomes
Macromolecule	beta-glucosidase (protein)
Unique Ligands	BGC, GLC, NA, NHE

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3WH7 \| pdb_00003wh7	Download File View File

Crystal structure of GH1 beta-glucosidase Td2F2 L-fucose complex

Jo, T., Fushinobu, S., Uchiyama, T., Yaoi, K.

(2016) FEBS J 283: 2340-2353

Released	2014-09-03
Method	X-RAY DIFFRACTION 1.1 Å
Organisms	metagenomes
Macromolecule	beta-glucosidase (protein)
Unique Ligands	FCB, NA, NHE

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3WH8 \| pdb_00003wh8	Download File View File

Crystal structure of GH1 beta-glucosidase Td2F2 isofagomine complex

Jo, T., Fushinobu, S., Uchiyama, T., Yaoi, K.

(2016) FEBS J 283: 2340-2353

Released	2014-09-03
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	metagenomes
Macromolecule	beta-glucosidase (protein)
Unique Ligands	GOL, IFM, NA, NHE

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4E9V \| pdb_00004e9v	Download File View File

Multicopper Oxidase mgLAC (data1)

Komori, H., Miyazaki, K., Higuchi, Y.

(2014) Acta Crystallogr D Biol Crystallogr 70: 772-779

Released	2013-03-27
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	uncultured bacterium
Macromolecule	Multicopper oxidase (protein)
Unique Ligands	CL, CU, O, OH

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4E9W \| pdb_00004e9w	Download File View File

Multicopper Oxidase mgLAC (data2)

Komori, H., Miyazaki, K., Higuchi, Y.

(2014) Acta Crystallogr D Biol Crystallogr 70: 772-779

Released	2013-03-27
Method	X-RAY DIFFRACTION 1.45 Å
Organisms	uncultured bacterium
Macromolecule	Multicopper oxidase (protein)
Unique Ligands	CL, CU, O, OXY

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4E9X \| pdb_00004e9x	Download File View File

Multicopper Oxidase mgLAC (data3)

Komori, H., Miyazaki, K., Higuchi, Y.

(2014) Acta Crystallogr D Biol Crystallogr 70: 772-779

Released	2013-03-27
Method	X-RAY DIFFRACTION 1.14 Å
Organisms	uncultured bacterium
Macromolecule	Multicopper oxidase (protein)
Unique Ligands	CL, CU, OXY

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4E9Y \| pdb_00004e9y	Download File View File

Multicopper Oxidase mgLAC (data4)

Komori, H., Miyazaki, K., Higuchi, Y.

(2014) Acta Crystallogr D Biol Crystallogr 70: 772-779

Released	2013-03-27
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	uncultured bacterium
Macromolecule	Multicopper oxidase (protein)
Unique Ligands	CL, CU, OXY

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4NER \| pdb_00004ner	Download File View File

Multicopper Oxidase CueO (data1)

Komori, H., Kataoka, K., Sakurai, T., Higuchi, Y.

(2014) Acta Crystallogr D Biol Crystallogr 70: 772-779

Released	2014-03-12
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Escherichia coli K-12
Macromolecule	Blue copper oxidase CueO (protein)
Unique Ligands	CU, O, OH

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5AYB \| pdb_00005ayb	Download File View File

Crystal structure of GH1 Beta-Glucosidase TD2F2 N223G mutant

Jo, T., Manninen, J.A., Matsuzawa, T., Uchiyama, T., Yaoi, K., Arakawa, T., Fushinobu, S.

(2016) FEBS J 283: 2340-2353

Released	2016-04-27
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	metagenomes
Macromolecule	BETA-GLUCOSIDASE (protein)
Unique Ligands	EDO, NA, NHE

1 to 25 of 32 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

1IDM | pdb_00001idm

1IPD | pdb_00001ipd

1OSI | pdb_00001osi

1OSJ | pdb_00001osj

1XAA | pdb_00001xaa

1XAB | pdb_00001xab

2DCY | pdb_00002dcy

2DCZ | pdb_00002dcz

2EBS | pdb_00002ebs

2ZWN | pdb_00002zwn

3A0F | pdb_00003a0f

3AYU | pdb_00003ayu

3UG3 | pdb_00003ug3

3UG4 | pdb_00003ug4

3UG5 | pdb_00003ug5

3WH5 | pdb_00003wh5

3WH6 | pdb_00003wh6

3WH7 | pdb_00003wh7

3WH8 | pdb_00003wh8

4E9V | pdb_00004e9v

4E9W | pdb_00004e9w

4E9X | pdb_00004e9x

4E9Y | pdb_00004e9y

4NER | pdb_00004ner

5AYB | pdb_00005ayb