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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Suzuki, R."

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Search Summary

This query matches 98 Structures.

Refinements

Structure Determination Methodology

experimental (98)

Scientific Name of Source Organism

	Homo sapiens (21)
	Severe acute respiratory syndrome coronavirus 2 (18)
	Crocosphaera subtropica ATCC 51142 (15)
	Bifidobacterium breve (8)
	Paenibacillus sp. 598K (7)
	Streptomyces olivaceoviridis (7)
	Bifidobacterium bifidum JCM 1254 (6)
	Lumbricus terrestris (6)
	Niallia circulans (6)
	Bifidobacterium longum (4)

More...

Taxonomy

	Bacteria (55)
	Eukaryota (35)
	Riboviria (18)
	Archaea (1)

Experimental Method

	X-RAY DIFFRACTION (76)
	ELECTRON MICROSCOPY (16)
	SOLUTION NMR (6)

Polymer Entity Type

Protein (98)

Refinement Resolution (Å)

	1.0 - 1.5 (2)
	1.5 - 2.0 (33)
	2.0 - 2.5 (24)
	2.5 - 3.0 (20)
	3.0 - 3.5 (12)
	3.5 - 4.0 (1)

Release Date

	2000 - 2004 (1)
	2005 - 2009 (16)
	2010 - 2014 (22)
	2015 - 2019 (29)
	2020 - 2024 (30)

Enzyme Classification Name

	Hydrolases (34)
	Transferases (35)
	Lyases (8)
	Oxidoreductases (3)
	Ligases (2)
	Isomerases (1)

Symmetry Type

	Asymmetric (73)
	Cyclic (31)

SCOP Classification

	All beta proteins (13)
	Alpha and beta proteins (a/b) (9)
	All alpha proteins (2)
	Alpha and beta proteins (a+b) (4)
	Artifacts (4)
	Small proteins (1)

AllSelected

1 to 25 of 98 Structures

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1IX5 \| pdb_00001ix5	Download File View File

Solution structure of the Methanococcus thermolithotrophicus FKBP

Suzuki, R., Nagata, K., Kawakami, M., Nemoto, N., Furutani, M., Adachi, K., Maruyama, T., Tanokura, M.

(2003) J Mol Biology 328: 1149-1160

Released	2003-06-10
Method	SOLUTION NMR
Organisms	Methanothermococcus thermolithotrophicus
Macromolecule	FKBP (protein)

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2D1Z \| pdb_00002d1z	Download File View File

Crystal structure of catalytic-site mutant xylanase from Streptomyces olivaceoviridis E-86

Suzuki, R., Kuno, A., Fujimoto, Z., Ito, S., Kawahara, S.I., Kaneko, S., Hasegawa, T., Taira, K.

(2009) J Biochem 146: 61-70

Released	2006-10-10
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Streptomyces olivaceoviridis
Macromolecule	ENDO-1,4-BETA-D-XYLANASE (protein)
Unique Ligands	GOL, SO4

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2D20 \| pdb_00002d20	Download File View File

Crystal structure of michaelis complex of catalytic-site mutant xylanase from Streptomyces olivaceoviridis E-86

Suzuki, R., Kuno, A., Fujimoto, Z., Ito, S., Kawahara, S.I., Kaneko, S., Hasegawa, T., Taira, K.

(2009) J Biochem 146: 61-70

Released	2006-10-10
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Streptomyces olivaceoviridis
Macromolecule	ENDO-1,4-BETA-D-XYLANASE (protein)
Unique Ligands	GOL, NPO
Unique branched monosaccharides	XYS

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2D22 \| pdb_00002d22	Download File View File

Crystal structure of covalent glycosyl-enzyme intermediate of catalytic-site mutant xylanase from Streptomyces olivaceoviridis E-86

Suzuki, R., Kuno, A., Fujimoto, Z., Ito, S., Kawahara, S.I., Kaneko, S., Hasegawa, T., Taira, K.

(2009) J Biochem 146: 61-70

Released	2006-10-10
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Streptomyces olivaceoviridis
Macromolecule	ENDO-1,4-BETA-D-XYLANASE (protein)
Unique Ligands	GOL, SO4
Unique branched monosaccharides	XYS

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2D23 \| pdb_00002d23	Download File View File

Crystal structure of EP complex of catalytic-site mutant xylanase from Streptomyces olivaceoviridis E-86

Suzuki, R., Kuno, A., Fujimoto, Z., Ito, S., Kawahara, S.I., Kaneko, S., Hasegawa, T., Taira, K.

(2009) J Biochem 146: 61-70

Released	2006-10-10
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Streptomyces olivaceoviridis
Macromolecule	ENDO-1,4-BETA-D-XYLANASE (protein)
Unique Ligands	AZI, GOL
Unique branched monosaccharides	XYS

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2D24 \| pdb_00002d24	Download File View File

Crystal structure of ES complex of catalytic-site mutant xylanase from Streptomyces olivaceoviridis E-86

Suzuki, R., Kuno, A., Fujimoto, Z., Ito, S., Kawahara, S.I., Kaneko, S., Hasegawa, T., Taira, K.

(2009) J Biochem 146: 61-70

Released	2006-10-10
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Streptomyces olivaceoviridis
Macromolecule	ENDO-1,4-BETA-D-XYLANASE (protein)
Unique Ligands	GOL, SO4
Unique branched monosaccharides	XYS

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2DRY \| pdb_00002dry	Download File View File

Crystal structure of the earthworm lectin C-terminal domain mutant

Suzuki, R., Fujimoto, Z.

(2007) J Biochem 141: 389-399

Released	2007-02-06
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Lumbricus terrestris
Macromolecule	29-kDa galactose-binding lectin (protein)
Unique Ligands	PGE, SO4

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2DRZ \| pdb_00002drz	Download File View File

Crystal structure of the earthworm lectin C-terminal domain mutant in complex with lactose

Suzuki, R., Fujimoto, Z.

(2007) J Biochem 141: 389-399

Released	2007-02-06
Method	X-RAY DIFFRACTION 2.19 Å
Organisms	Lumbricus terrestris
Macromolecule	29-kDa galactose-binding lectin (protein)
Unique Ligands	SO4
Unique branched monosaccharides	BGC, GAL

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2DS0 \| pdb_00002ds0	Download File View File

Crystal structure of the earthworm lectin C-terminal domain mutant in complex with 6'-sialyllactose

Suzuki, R., Fujimoto, Z.

(2007) J Biochem 141: 389-399

Released	2007-02-06
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Lumbricus terrestris
Macromolecule	29-kDa galactose-binding lectin (protein)
Unique Ligands	SO4
Unique branched monosaccharides	BGC, GAL, SIA

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2RNN \| pdb_00002rnn	Download File View File

Solution Structure of the N-terminal SAP Domain of SUMO E3 Ligases from Saccharomyces cerevisiae

Suzuki, R., Shindo, H., Tase, A., Yamazaki, T.

(2009) Proteins 75: 336-347

Released	2008-12-30
Method	SOLUTION NMR
Organisms	Saccharomyces cerevisiae
Macromolecule	E3 SUMO-protein ligase SIZ1 (protein)

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2RNO \| pdb_00002rno	Download File View File

Solution Structure of the N-terminal SAP Domain of SUMO E3 Ligases from Oryza sativa

Suzuki, R., Shindo, H., Tase, A., Yamazaki, T.

(2009) Proteins 75: 336-347

Released	2008-12-30
Method	SOLUTION NMR
Organisms	Oryza sativa Japonica Group
Macromolecule	Putative DNA-binding protein (protein)

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2RQF \| pdb_00002rqf	Download File View File

Solution structure of juvenile hormone binding protein from silkworm in complex with JH III

Suzuki, R., Fujimoto, Z., Shiotsuki, T., Momma, M., Tase, A., Yamazaki, T.

(2011) Sci Rep 1: 133-133

Released	2010-05-05
Method	SOLUTION NMR
Organisms	Bombyx mori
Macromolecule	Hemolymph juvenile hormone binding protein (protein)
Unique Ligands	JH3

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2RSD \| pdb_00002rsd	Download File View File

Solution structure of the plant homeodomain (PHD) of the E3 SUMO ligase Siz1 from rice

Shindo, H., Tsuchiya, W., Suzuki, R., Yamazaki, T.

(2012) FEBS Lett 586: 1783-1789

Released	2012-08-15
Method	SOLUTION NMR
Organisms	Oryza sativa Japonica Group
Macromolecule	E3 SUMO-protein ligase SIZ1 (protein)
Unique Ligands	ZN

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2RST \| pdb_00002rst	Download File View File

NMR structure of the C-terminal domain of EW29

Hemmi, H.

(2013) FEBS J 280: 70-82

Released	2013-04-17
Method	SOLUTION NMR
Organisms	Lumbricus terrestris
Macromolecule	29-kDa galactose-binding lectin (protein)

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2Z8D \| pdb_00002z8d	Download File View File

The galacto-N-biose-/lacto-N-biose I-binding protein (GL-BP) of the ABC transporter from Bifidobacterium longum in complex with lacto-N-biose

Suzuki, R., Wada, J., Katayama, T., Fushinobu, S.

(2008) J Biological Chem 283: 13165-13173

Released	2008-03-18
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Bifidobacterium longum
Macromolecule	Galacto-N-biose/lacto-N-biose I transporter substrate-binding protein (protein)
Unique Ligands	MES, ZN
Unique branched monosaccharides	GAL, NAG

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2Z8E \| pdb_00002z8e	Download File View File

The galacto-N-biose-/lacto-N-biose I-binding protein (GL-BP) of the ABC transporter from Bifidobacterium longum in complex with galacto-N-biose

Suzuki, R., Wada, J., Katayama, T., Fushinobu, S.

(2008) J Biological Chem 283: 13165-13173

Released	2008-03-18
Method	X-RAY DIFFRACTION 1.99 Å
Organisms	Bifidobacterium longum
Macromolecule	Galacto-N-biose/lacto-N-biose I transporter substrate-binding protein (protein)
Unique Ligands	MES, ZN
Unique branched monosaccharides	GAL, NGA

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2Z8F \| pdb_00002z8f	Download File View File

The galacto-N-biose-/lacto-N-biose I-binding protein (GL-BP) of the ABC transporter from Bifidobacterium longum in complex with lacto-N-tetraose

Suzuki, R., Wada, J., Katayama, T., Fushinobu, S.

(2008) J Biological Chem 283: 13165-13173

Released	2008-03-18
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Bifidobacterium longum
Macromolecule	Galacto-N-biose/lacto-N-biose I transporter substrate-binding protein (protein)
Unique Ligands	MES, NA, ZN
Unique branched monosaccharides	BGC, GAL, NAG

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2ZQN \| pdb_00002zqn	Download File View File

Crystal structure of the earthworm R-type lectin C-half in complex with Lactose

Suzuki, R., Kuno, A., Hasegawa, T., Hirabayashi, J., Kasai, K., Momma, M., Fujimoto, Z.

(2009) Acta Crystallogr D Biol Crystallogr 65: 49-57

Released	2008-09-02
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Lumbricus terrestris
Macromolecule	29-kDa galactose-binding lectin (protein)
Unique Ligands	IMD, PO4
Unique branched monosaccharides	BGC, GAL

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2ZQO \| pdb_00002zqo	Download File View File

Crystal structure of the earthworm R-type lectin C-half in complex with GalNAc

Suzuki, R., Kuno, A., Hasegawa, T., Hirabayashi, J., Kasai, K., Momma, M., Fujimoto, Z.

(2009) Acta Crystallogr D Biol Crystallogr 65: 49-57

Released	2008-09-02
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Lumbricus terrestris
Macromolecule	29-kDa galactose-binding lectin (protein)
Unique Ligands	CD, IMD, NGA, PO4

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2ZXQ \| pdb_00002zxq	Download File View File

Crystal structure of endo-alpha-N-acetylgalactosaminidase from Bifidobacterium longum (EngBF)

Suzuki, R., Katayama, T., Ashida, H., Yamamoto, K., Kitaoka, M., Fushinobu, S.

(2009) J Biochem

Released	2009-06-16
Method	X-RAY DIFFRACTION 2 Å
Organisms	Bifidobacterium longum
Macromolecule	Endo-alpha-N-acetylgalactosaminidase (protein)
Unique Ligands	MN, MPD

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3A1Z \| pdb_00003a1z	Download File View File

Crystal structure of juvenile hormone binding protein from silkworm

Suzuki, R., Fujimoto, Z., Shiotsuki, T., Momma, M., Tase, A., Yamazaki, T.

(2013) PLoS One 8: e56261-e56261

Released	2010-04-28
Method	X-RAY DIFFRACTION 2.59 Å
Organisms	Bombyx mori
Macromolecule	Hemolymph juvenile hormone binding protein (protein)
Unique Ligands	MPD, ZN

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3AHC \| pdb_00003ahc	Download File View File

Resting form of Phosphoketolase from Bifidobacterium Breve

Suzuki, R., Katayama, T., Kim, B.-J., Wakagi, T., Shoun, H., Ashida, H., Yamamoto, K., Fushinobu, S.

(2010) J Biological Chem 285: 34279-34287

Released	2010-08-25
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Bifidobacterium breve
Macromolecule	Xylulose 5-phosphate/fructose 6-phosphate phosphoketolase (protein)
Unique Ligands	2PE, EDO, MG, NA, TPP

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3AHD \| pdb_00003ahd	Download File View File

Phosphoketolase from Bifidobacterium Breve complexed with 2-acetyl-thiamine diphosphate

Suzuki, R., Katayama, T., Kim, B.-J., Wakagi, T., Shoun, H., Ashida, H., Yamamoto, K., Fushinobu, S.

(2010) J Biological Chem 285: 34279-34287

Released	2010-08-25
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Bifidobacterium breve
Macromolecule	Xylulose 5-phosphate/fructose 6-phosphate phosphoketolase (protein)
Unique Ligands	EDO, HTL, MG, NA

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3AHE \| pdb_00003ahe	Download File View File

Phosphoketolase from Bifidobacterium Breve complexed with dihydroxyethyl thiamine diphosphate

Suzuki, R., Katayama, T., Kim, B.-J., Wakagi, T., Shoun, H., Ashida, H., Yamamoto, K., Fushinobu, S.

(2010) J Biological Chem 285: 34279-34287

Released	2010-08-25
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Bifidobacterium breve
Macromolecule	Xylulose 5-phosphate/fructose 6-phosphate phosphoketolase (protein)
Unique Ligands	2PE, EDO, MG, NA, THD

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3AHF \| pdb_00003ahf	Download File View File

Phosphoketolase from Bifidobacterium Breve complexed with inorganic phosphate

Suzuki, R., Katayama, T., Kim, B.-J., Wakagi, T., Shoun, H., Ashida, H., Yamamoto, K., Fushinobu, S.

(2010) J Biological Chem 285: 34279-34287

Released	2010-08-25
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Bifidobacterium breve
Macromolecule	Xylulose 5-phosphate/fructose 6-phosphate phosphoketolase (protein)
Unique Ligands	GOL, MG, PO4, TPP

1 to 25 of 98 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

1IX5 | pdb_00001ix5

2D1Z | pdb_00002d1z

2D20 | pdb_00002d20

2D22 | pdb_00002d22

2D23 | pdb_00002d23

2D24 | pdb_00002d24

2DRY | pdb_00002dry

2DRZ | pdb_00002drz

2DS0 | pdb_00002ds0

2RNN | pdb_00002rnn

2RNO | pdb_00002rno

2RQF | pdb_00002rqf

2RSD | pdb_00002rsd

2RST | pdb_00002rst

2Z8D | pdb_00002z8d

2Z8E | pdb_00002z8e

2Z8F | pdb_00002z8f

2ZQN | pdb_00002zqn

2ZQO | pdb_00002zqo

2ZXQ | pdb_00002zxq

3A1Z | pdb_00003a1z

3AHC | pdb_00003ahc

3AHD | pdb_00003ahd

3AHE | pdb_00003ahe

3AHF | pdb_00003ahf