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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Hattori, Y."

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Search Summary

This query matches 17 Structures.

Refinements

Structure Determination Methodology

experimental (17)

Scientific Name of Source Organism

	Severe acute respiratory syndrome-related coronavirus (7)
	Homo sapiens (5)
	synthetic construct (3)
	Equus caballus (2)
	Schizosaccharomyces pombe 972h- (1)
	Staphylococcus aureus (1)

Taxonomy

	Eukaryota (8)
	Riboviria (7)
	other sequences (3)
	Bacteria (1)

Experimental Method

	X-RAY DIFFRACTION (15)
	SOLUTION NMR (2)

Polymer Entity Type

	Protein (16)
	DNA (1)

Refinement Resolution (Å)

	1.0 - 1.5 (1)
	1.5 - 2.0 (3)
	2.0 - 2.5 (9)
	2.5 - 3.0 (1)
	3.0 - 3.5 (1)

Release Date

	2010 - 2014 (7)
	2015 - 2019 (8)
	2020 - 2024 (2)

Enzyme Classification Name

	Hydrolases (9)
	Oxidoreductases (2)
	Isomerases (1)

Symmetry Type

	Asymmetric (9)
	Cyclic (7)

SCOP Classification

	All beta proteins (8)
	All alpha proteins (2)
	Alpha and beta proteins (a+b) (2)
	Artifacts (1)

AllSelected

1 to 17 of 17 Structures

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2ND5 \| pdb_00002nd5	Download File View File

Lysine dimethylated FKBP12

Hattori, Y., Sebera, J., Sychrovsky, V., Furuita, K., Sugiki, T., Ohki, I., Ikegami, T., Kobayashi, N., Tanaka, Y., Fujiwara, T., Kojima, C.

To be published

Released	2017-05-17
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Peptidyl-prolyl cis-trans isomerase FKBP1A (protein)

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2RUJ \| pdb_00002ruj	Download File View File

Solution structure of MTSL spin-labeled Schizosaccharomyces pombe Sin1 CRIM domain

Furuita, K., Kataoka, S., Sugiki, T., Kobayashi, N., Ikegami, T., Shiozaki, K., Fujiwara, T., Kojima, C.

(2015) J Biomol NMR 61: 55-64

Released	2015-07-29
Method	SOLUTION NMR
Organisms	Schizosaccharomyces pombe 972h-
Macromolecule	Stress-activated map kinase-interacting protein 1 (protein)

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3ATW \| pdb_00003atw	Download File View File

Structure-Based Design, Synthesis, Evaluation of Peptide-mimetic SARS 3CL Protease Inhibitors

Akaji, K., Konno, H., Mitsui, H., Teruya, K., Hattori, Y., Ozaki, T., Kusunoki, M., Sanjho, A.

(2011) J Med Chem 54: 7962-7973

Released	2011-12-14
Method	X-RAY DIFFRACTION 2.36 Å
Organisms	Severe acute respiratory syndrome-related coronavirus
Macromolecule	3C-Like Proteinase (protein) peptide ACE-THR-VAL-ALC-HIS-H (protein)

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3AVZ \| pdb_00003avz	Download File View File

Structure of SARS 3CL protease with peptidic aldehyde inhibitor containing cyclohexyl side chain

Akaji, K., Konno, H., Mitsui, H., Teruya, K., Hattori, Y., Ozaki, T., Kusunoki, M., Sanjho, A.

(2011) J Med Chem 54: 7962-7973

Released	2011-12-14
Method	X-RAY DIFFRACTION 2.46 Å
Organisms	Severe acute respiratory syndrome-related coronavirus
Macromolecule	3C-Like Proteinase (protein) peptide ACE-SER-ALA-VAL-ALC-HIS-H (protein)

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3AW0 \| pdb_00003aw0	Download File View File

Structure of SARS 3CL protease with peptidic aldehyde inhibitor

Akaji, K., Konno, H., Mitsui, H., Teruya, K., Hattori, Y., Ozaki, T., Kusunoki, M., Sanjho, A.

(2011) J Med Chem 54: 7962-7973

Released	2011-12-14
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Severe acute respiratory syndrome-related coronavirus
Macromolecule	3C-Like Proteinase (protein) peptide ACE-SER-ALA-VAL-LEU-HIS-H (protein)

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3AW1 \| pdb_00003aw1	Download File View File

Structure of SARS 3CL protease auto-proteolysis resistant mutant in the absent of inhibitor

Akaji, K., Konno, H., Mitsui, H., Teruya, K., Hattori, Y., Ozaki, T., Kusunoki, M., Sanjho, A.

(2011) J Med Chem 54: 7962-7973

Released	2011-12-14
Method	X-RAY DIFFRACTION 2 Å
Organisms	Severe acute respiratory syndrome-related coronavirus
Macromolecule	3C-Like Proteinase (protein)

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3GP7 \| pdb_00003gp7	Download File View File

Staphylococcal Enterotoxin B mutant N23YK97SK98S

Yanaka, S., Tanaka, Y., Tsumoto, K.

(2010) Protein Eng Des Sel 23: 415-421

Released	2010-03-09
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Staphylococcus aureus
Macromolecule	Enterotoxin type B (protein)

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3NBS \| pdb_00003nbs	Download File View File

Crystal structure of dimeric cytochrome c from horse heart

Taketa, M., Komori, H., Hirota, S., Higuchi, Y.

(2010) Proc Natl Acad Sci U S A 107: 12854-12859

Released	2010-07-14
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Equus caballus
Macromolecule	Cytochrome c (protein)
Unique Ligands	HEC, PEG, PG4, PO4

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3NBT \| pdb_00003nbt	Download File View File

Crystal structure of trimeric cytochrome c from horse heart

Taketa, M., Komori, H., Hirota, S., Higuchi, Y.

(2010) Proc Natl Acad Sci U S A 107: 12854-12859

Released	2010-07-14
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Equus caballus
Macromolecule	Cytochrome c (protein)
Unique Ligands	HEC, PEG, PG4, PGE

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4TRW \| pdb_00004trw	Download File View File

Structure of BACE1 complex with a syn-HEA-type inhibitor

Akaji, K., Teruya, K., Akiyama, T., Sanjho, A., Yamashita, E., Nakagawa, A.

(2015) Bioorg Med Chem 23: 5626-5640

Released	2015-07-01
Method	X-RAY DIFFRACTION 2.85 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Beta-secretase 1 (protein) L-alpha-glutamyl-L-isoleucyl-N-[(2R,3S)-1-{[(1S)-1-carboxybutyl]amino}-2-hydroxy-5-methylhexan-3-yl]-3-thiophen-2-yl-L-alaninamide (protein)

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4TRZ \| pdb_00004trz	Download File View File

Structure of BACE1 complex with 2-thiophenyl HEA-type inhibitor

Akaji, K., Teruya, K., Akiyama, T., Sanjho, A., Yamashita, E., Nakagawa, A.

(2015) Bioorg Med Chem 23: 5626-5640

Released	2015-07-01
Method	X-RAY DIFFRACTION 3.25 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	2-thiophenyl HEA-type inhibitor (protein) Beta-secretase 1 (protein)

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4TWW \| pdb_00004tww	Download File View File

Structure of SARS-3CL protease complex with a Bromobenzoyl (S,R)-N-decalin type inhibitor

Akaji, K., Teruya, K., Shimamoto, Y., Sanjho, A., Yamashita, E., Nakagawa, A.

(2015) Bioorg Med Chem 23: 876-890

Released	2015-02-18
Method	X-RAY DIFFRACTION 2.42 Å
Organisms	Severe acute respiratory syndrome-related coronavirus
Macromolecule	3C-like proteinase (protein)
Unique Ligands	3A7

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4TWY \| pdb_00004twy	Download File View File

Structure of SARS-3CL protease complex with a phenylbenzoyl (S,R)-N-decalin type inhibitor

Akaji, K., Teruya, K., Shimamoto, Y., Sanjho, A., Yamashita, E., Nakagawa, A.

(2015) Bioorg Med Chem 23: 876-890

Released	2015-02-18
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Severe acute respiratory syndrome-related coronavirus
Macromolecule	3C-like proteinase (protein)
Unique Ligands	3BL

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4WY3 \| pdb_00004wy3	Download File View File

Structure of SARS-3CL protease complex with a phenylbenzoyl (R,S)-N-decalin type inhibitor

Akaji, K., Teruya, K., Shimamoto, Y., Sanjho, A., Yamashita, E., Nakagawa, A.

(2015) Bioorg Med Chem 23: 876-890

Released	2015-02-18
Method	X-RAY DIFFRACTION 1.89 Å
Organisms	Severe acute respiratory syndrome-related coronavirus
Macromolecule	3C-like proteinase (protein)
Unique Ligands	3X5

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5IX7 \| pdb_00005ix7	Download File View File

Crystal structure of metallo-DNA nanowire with infinite one-dimensional silver array

Kondo, J., Tada, Y., Dairaku, T., Hattori, Y., Saneyoshi, H., Ono, A., Tanaka, Y.

(2017) Nat Chem 9: 956-960

Released	2017-07-05
Method	X-RAY DIFFRACTION 1.398 Å
Organisms	synthetic construct
Macromolecule	DNA (5'-D(GPGPAPCPTP(CBR)PGPAPCPTPCPC)-3') (nucleic acid)
Unique Ligands	AG, K

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7E0G \| pdb_00007e0g	Download File View File

Crystal structure of Lysine Specific Demethylase 1 (LSD1) with TAK-418, FAD-adduct

Oki, H.

(2021) Sci Adv 7:

Released	2021-03-24
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Homo sapiens
Macromolecule	Lysine-specific histone demethylase 1A (protein)
Unique Ligands	GOL, HUF, IMD, MG

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7XW8 \| pdb_00007xw8	Download File View File

Crystal structure of Lysine Specific Demethylase 1 (LSD1) with TAK-418 distomer, FAD-adduct

Oki, H.

(2022) Eur J Med Chem 239: 114522-114522

Released	2022-10-12
Method	X-RAY DIFFRACTION 2.28 Å
Organisms	Homo sapiens
Macromolecule	Lysine-specific histone demethylase 1A (protein)
Unique Ligands	FA8, GOL, I00, MG

1 to 17 of 17 Structures

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

2ND5 | pdb_00002nd5

Lysine dimethylated FKBP12

2RUJ | pdb_00002ruj

Solution structure of MTSL spin-labeled Schizosaccharomyces pombe Sin1 CRIM domain

3ATW | pdb_00003atw

Structure-Based Design, Synthesis, Evaluation of Peptide-mimetic SARS 3CL Protease Inhibitors

3AVZ | pdb_00003avz

Structure of SARS 3CL protease with peptidic aldehyde inhibitor containing cyclohexyl side chain

3AW0 | pdb_00003aw0

Structure of SARS 3CL protease with peptidic aldehyde inhibitor

3AW1 | pdb_00003aw1

Structure of SARS 3CL protease auto-proteolysis resistant mutant in the absent of inhibitor

3GP7 | pdb_00003gp7

Staphylococcal Enterotoxin B mutant N23YK97SK98S

3NBS | pdb_00003nbs

Crystal structure of dimeric cytochrome c from horse heart

3NBT | pdb_00003nbt

Crystal structure of trimeric cytochrome c from horse heart

4TRW | pdb_00004trw

Structure of BACE1 complex with a syn-HEA-type inhibitor

4TRZ | pdb_00004trz

Structure of BACE1 complex with 2-thiophenyl HEA-type inhibitor

4TWW | pdb_00004tww

Structure of SARS-3CL protease complex with a Bromobenzoyl (S,R)-N-decalin type inhibitor

4TWY | pdb_00004twy

Structure of SARS-3CL protease complex with a phenylbenzoyl (S,R)-N-decalin type inhibitor

4WY3 | pdb_00004wy3

Structure of SARS-3CL protease complex with a phenylbenzoyl (R,S)-N-decalin type inhibitor

5IX7 | pdb_00005ix7

Crystal structure of metallo-DNA nanowire with infinite one-dimensional silver array

7E0G | pdb_00007e0g

Crystal structure of Lysine Specific Demethylase 1 (LSD1) with TAK-418, FAD-adduct

7XW8 | pdb_00007xw8

Crystal structure of Lysine Specific Demethylase 1 (LSD1) with TAK-418 distomer, FAD-adduct

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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

2ND5 | pdb_00002nd5

2RUJ | pdb_00002ruj

3ATW | pdb_00003atw

3AVZ | pdb_00003avz

3AW0 | pdb_00003aw0

3AW1 | pdb_00003aw1

3GP7 | pdb_00003gp7

3NBS | pdb_00003nbs

3NBT | pdb_00003nbt

4TRW | pdb_00004trw

4TRZ | pdb_00004trz

4TWW | pdb_00004tww

4TWY | pdb_00004twy

4WY3 | pdb_00004wy3

5IX7 | pdb_00005ix7

7E0G | pdb_00007e0g

7XW8 | pdb_00007xw8