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233,249 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Tsuda, S."

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Search Summary

This query matches 36 Structures.

Refinements

Structure Determination Methodology

experimental (36)

Scientific Name of Source Organism

	Zoarces elongatus (8)
	Typhula ishikariensis (4)
	Bacillus subtilis (3)
	Antarctomyces psychrotrophicus (2)
	Gallus gallus (2)
	Geotrichum sp. M128 (2)
	Homo sapiens (2)
	Hypomesus nipponensis (2)
	Lycodichthys dearborni (2)
	Pachycara brachycephalum (2)

More...

Taxonomy

	Eukaryota (32)
	Bacteria (4)

Experimental Method

	X-RAY DIFFRACTION (23)
	SOLUTION NMR (13)

Polymer Entity Type

Protein (36)

Refinement Resolution (Å)

	0.5 - 1.0 (3)
	1.0 - 1.5 (12)
	1.5 - 2.0 (5)
	2.0 - 2.5 (2)
	2.5 - 3.0 (1)

Release Date

	1995 - 1999 (4)
	2000 - 2004 (8)
	2005 - 2009 (6)
	2010 - 2014 (4)
	2015 - 2019 (9)
	2020 - 2024 (5)

Enzyme Classification Name

Hydrolases (9)

Membrane Protein Annotation

OPM (6)

Symmetry Type

	Asymmetric (32)
	Cyclic (5)

SCOP Classification

	All beta proteins (16)
	Alpha and beta proteins (a+b) (6)
	Artifacts (4)
	All alpha proteins (2)
	Alpha and beta proteins (a/b) (1)
	Small proteins (1)

AllSelected

1 to 25 of 36 Structures

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1C89 \| pdb_00001c89	Download File View File

NMR STRUCTURE OF INTRAMOLECULAR DIMER ANTIFREEZE PROTEIN RD3, 40 SA STRUCTURES

Miura, K., Tsuda, S.

(2001) J Biological Chem 276: 1304-1310

Released	2001-02-28
Method	SOLUTION NMR
Organisms	Pachycara brachycephalum
Macromolecule	ANTIFREEZE PROTEIN TYPE III (protein)

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1C8A \| pdb_00001c8a	Download File View File

NMR STRUCTURE OF INTRAMOLECULAR DIMER ANTIFREEZE PROTEIN RD3, 40 SA STRUCTURES

Miura, K., Tsuda, S.

(2001) J Biological Chem 276: 1304-1310

Released	2001-02-28
Method	SOLUTION NMR
Organisms	Pachycara brachycephalum
Macromolecule	PROTEIN (ANTIFREEZE PROTEIN TYPE III) (protein)

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1DQC \| pdb_00001dqc	Download File View File

SOLUTION STRUCTURE OF TACHYCITIN, AN ANTIMICROBIAL PROTEIN WITH CHITIN-BINDING FUNCTION

Suetake, T., Tsuda, S., Kawabata, S., Miura, K., Kawano, K.

(2000) J Biological Chem 275: 17929-17932

Released	2000-09-13
Method	SOLUTION NMR
Organisms	Tachypleus tridentatus
Macromolecule	TACHYCITIN (protein)

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1I56 \| pdb_00001i56	Download File View File

SOLUTION STRUCTURE OF CA2+-BOUND STATE OF CANINE MILK LYSOZYME

Kobashigawa, Y., Tsuda, S., Nitta, K.

To be published

Released	2002-02-27
Method	SOLUTION NMR
Organisms	Canis lupus familiaris
Macromolecule	LYSOZYME C (protein)

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1ISP \| pdb_00001isp	Download File View File

Crystal structure of Bacillus subtilis lipase at 1.3A resolution

Kawasaki, K., Kondo, H., Suzuki, M., Ohgiya, S., Tsuda, S.

(2002) Acta Crystallogr D Biol Crystallogr 58: 1168-1174

Released	2002-12-19
Method	X-RAY DIFFRACTION 1.3 Å
Organisms	Bacillus subtilis
Macromolecule	lipase (protein)
Unique Ligands	GOL

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1IY3 \| pdb_00001iy3	Download File View File

Solution Structure of the Human lysozyme at 4 degree C

Kumeta, H., Miura, A., Kobashigawa, Y., Miura, K., Oka, C., Nitta, K., Nemoto, N., Tsuda, S.

(2003) Biochemistry 42: 1209-1216

Released	2002-07-31
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Lysozyme (protein)

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1IY4 \| pdb_00001iy4	Download File View File

Solution structure of the human lysozyme at 35 degree C

Kumeta, H., Miura, A., Kobashigawa, Y., Miura, K., Oka, C., Nitta, K., Nemoto, N., Tsuda, S.

(2003) Biochemistry 42: 1209-1216

Released	2002-07-31
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Lysozyme (protein)

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1SKT \| pdb_00001skt	Download File View File

SOLUTION STRUCTURE OF APO N-DOMAIN OF TROPONIN C, NMR, 40 STRUCTURES

Tsuda, S., Miura, A., Gagne, S.M., Spyracopoulos, L., Sykes, B.D.

(1999) Biochemistry 38: 5693-5700

Released	1998-12-09
Method	SOLUTION NMR
Organisms	Gallus gallus
Macromolecule	TROPONIN-C (protein)

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1SQJ \| pdb_00001sqj	Download File View File

Crystal Structure Analysis of Oligoxyloglucan reducing-end-specific cellobiohydrolase (OXG-RCBH)

Yaoi, K., Kondo, H., Noro, N., Suzuki, M., Tsuda, S., Mitsuishi, Y.

(2004) Structure 12: 1209-1217

Released	2004-07-20
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Geotrichum sp. M128
Macromolecule	oligoxyloglucan reducing-end-specific cellobiohydrolase (protein)

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1ZAC \| pdb_00001zac	Download File View File

N-DOMAIN OF TROPONIN C FROM CHICKEN SKELETAL MUSCLE, NMR, MINIMIZED AVERAGE STRUCTURE

Tsuda, S., Miura, A., Gagne, S.M., Spyracopoulos, L., Sykes, B.D.

(1999) Biochemistry 38: 5693-5700

Released	1998-11-11
Method	SOLUTION NMR
Organisms	Gallus gallus
Macromolecule	TROPONIN-C (protein)

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2CZQ \| pdb_00002czq	Download File View File

A novel cutinase-like protein from Cryptococcus sp.

Masaki, K., Kamini, N.R., Ikeda, H., Iefuji, H., Kondo, H., Suzuki, M., Tsuda, S.

(2009) Proteins 77: 710-717

Released	2006-07-14
Method	X-RAY DIFFRACTION 1.05 Å
Organisms	Cryptococcus sp. S-2
Macromolecule	cutinase-like protein (protein)
Unique Ligands	CIT, EDO

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2D56 \| pdb_00002d56	Download File View File

Solution Structure of ASABF, Antibacterial Peptide Isolated from a Nematode, Ascaris Suum

Nakano, M., Aizawa, T., Kamiya, M., Miura, K., Kumaki, Y., Demura, M., Tsuda, S., Kawano, K.

To be published

Released	2006-11-14
Method	SOLUTION NMR
Organisms	Ascaris suum
Macromolecule	ASABF (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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2LX2 \| pdb_00002lx2	Download File View File

1H,13C,15N assignments for an isoform of the type III antifreeze protein from notched-fin eelpout

Kumeta, H., Ogura, K., Nishimiya, Y., Miura, A., Inagaki, F., Tsuda, S.

(2013) J Biomol NMR 55: 225-230

Released	2013-07-24
Method	SOLUTION NMR
Organisms	Zoarces elongatus
Macromolecule	Type III antifreeze protein nfeAFP11 (protein)

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2LX3 \| pdb_00002lx3	Download File View File

1H,13C,15N assignments for an isoform of the type III antifreeze protein from notched-fin eelpout

Kumeta, H., Ogura, K., Nishimiya, Y., Miura, A., Inagaki, F., Tsuda, S.

(2013) J Biomol NMR 55: 225-230

Released	2013-07-24
Method	SOLUTION NMR
Organisms	Zoarces elongatus
Macromolecule	Type III antifreeze protein nfeAFP11 (protein)

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2ZIB \| pdb_00002zib	Download File View File

Crystal structure analysis of calcium-independent type II antifreeze protein

Nishimiya, Y., Sato, R., Kondo, H., Noro, N., Sugimoto, H., Suzuki, M., Tsuda, S.

(2008) J Mol Biology 382: 734-746

Released	2008-08-19
Method	X-RAY DIFFRACTION 1.34 Å
Organisms	Brachyopsis segaliensis
Macromolecule	Type II antifreeze protein (protein)
Unique Ligands	SO4

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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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3NLA \| pdb_00003nla	Download File View File

NMR STRUCTURE OF THE N-TERMINAL DOMAIN WITH A LINKER PORTION OF ANTARCTIC EEL POUT ANTIFREEZE PROTEIN RD3, 40 STRUCTURES

Miura, K., Ohgiya, S., Hoshino, T., Nemoto, N., Hikichi, K., Tsuda, S.

(1996) Nature 384: 285-288

Released	1999-02-23
Method	SOLUTION NMR
Organisms	Lycodichthys dearborni
Macromolecule	ANTIFREEZE PROTEIN RD3 TYPE III (protein)

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3RDN \| pdb_00003rdn	Download File View File

NMR STRUCTURE OF THE N-TERMINAL DOMAIN WITH A LINKER PORTION OF ANTARCTIC EEL POUT ANTIFREEZE PROTEIN RD3, MINIMIZED AVERAGE STRUCTURE

Miura, K., Ohgiya, S., Hoshino, T., Nemoto, N., Hikichi, K., Tsuda, S.

(1996) Nature 384: 285-288

Released	1999-02-23
Method	SOLUTION NMR
Organisms	Lycodichthys dearborni
Macromolecule	ANTIFREEZE PROTEIN RD3 TYPE III (protein)

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3VN3 \| pdb_00003vn3	Download File View File

Fungal antifreeze protein exerts hyperactivity by constructing an inequable beta-helix

Kondo, H., Xiao, N., Hanada, Y., Sugimoto, H., Hoshino, T., Garnham, C.P., Davies, P.L., Tsuda, S.

(2012) Proc Natl Acad Sci U S A 109: 9360-9365

Released	2012-06-06
Method	X-RAY DIFFRACTION 0.95 Å
Organisms	Typhula ishikariensis
Macromolecule	Antifreeze protein (protein)
Unique Ligands	EDO

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3WP9 \| pdb_00003wp9	Download File View File

Crystal structure of antifreeze protein from an Antarctic sea ice bacterium Colwellia sp.

Hanada, Y., Nishimiya, Y., Miura, A., Tsuda, S., Kondo, H.

(2014) FEBS J 281: 3576-3590

Released	2014-07-02
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Colwellia sp. SLW05
Macromolecule	Ice-binding protein (protein)

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5B5H \| pdb_00005b5h	Download File View File

Hydrophobic ice-binding site confer hyperactivity on antifreeze protein from a snow mold fungus

Cheng, J., Hanada, Y., Miura, A., Tsuda, S., Kondo, H.

(2016) Biochem J 473: 4011-4026

Released	2016-09-28
Method	X-RAY DIFFRACTION 1 Å
Organisms	Typhula ishikariensis
Macromolecule	Antifreeze protein (protein)
Unique Ligands	NA, SO4

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5XQN \| pdb_00005xqn	Download File View File

Crystal structure of Notched-fin eelpout type III antifreeze protein (NFE6, AFP), C2221 form.

Adachi, M., Kondo, H., Tsuda, S.

(2018) Proc Natl Acad Sci U S A 115: 5456-5461

Released	2018-05-16
Method	X-RAY DIFFRACTION 1.19 Å
Organisms	Zoarces elongatus
Macromolecule	Ice-structuring protein (protein)
Unique Ligands	SO4

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5XQP \| pdb_00005xqp	Download File View File

Crystal structure of Notched-fin eelpout type III antifreeze protein (NFE6, AFP), P212121 form

Adachi, M., Shimizu, R., Shibazaki, C., Kondo, H., Tsuda, S.

(2018) Proc Natl Acad Sci U S A 115: 5456-5461

Released	2018-05-16
Method	X-RAY DIFFRACTION 1 Å
Organisms	Zoarces elongatus
Macromolecule	Ice-structuring protein (protein)
Unique Ligands	SO4

1 to 25 of 36 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

1C89 | pdb_00001c89

1C8A | pdb_00001c8a

1DQC | pdb_00001dqc

1I56 | pdb_00001i56

1ISP | pdb_00001isp

1IY3 | pdb_00001iy3

1IY4 | pdb_00001iy4

1SKT | pdb_00001skt

1SQJ | pdb_00001sqj

1ZAC | pdb_00001zac

2CZQ | pdb_00002czq

2D56 | pdb_00002d56

2DCY | pdb_00002dcy

2DCZ | pdb_00002dcz

2LX2 | pdb_00002lx2

2LX3 | pdb_00002lx3

2ZIB | pdb_00002zib

3A0F | pdb_00003a0f

3NLA | pdb_00003nla

3RDN | pdb_00003rdn

3VN3 | pdb_00003vn3

3WP9 | pdb_00003wp9

5B5H | pdb_00005b5h

5XQN | pdb_00005xqn

5XQP | pdb_00005xqp