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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Hanada, K."

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Search Summary

This query matches 26 Structures.

Refinements

Structure Determination Methodology

experimental (26)

Scientific Name of Source Organism

	Homo sapiens (25)
	Glycine max (1)

Taxonomy

	Eukaryota (25)
	Eukaryota (eukaryotes) (1)

Experimental Method

	X-RAY DIFFRACTION (23)
	SOLUTION NMR (2)
	ELECTRON MICROSCOPY (1)

Polymer Entity Type

Protein (26)

Refinement Resolution (Å)

	1.0 - 1.5 (2)
	1.5 - 2.0 (16)
	2.0 - 2.5 (3)
	2.5 - 3.0 (2)
	3.5 - 4.0 (1)

Release Date

	2000 - 2004 (1)
	2005 - 2009 (9)
	2010 - 2014 (1)
	2015 - 2019 (11)
	2020 - 2024 (4)

Enzyme Classification Name

Hydrolases (4)

Membrane Protein Annotation

OPM (1)

Symmetry Type

	Asymmetric (22)
	Cyclic (4)

SCOP Classification

	All beta proteins (1)
	Small proteins (1)

AllSelected

1 to 25 of 26 Structures

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1JU8 \| pdb_00001ju8	Download File View File

Solution structure of Leginsulin, a plant hormon

Yamazaki, T., Takaoka, M., Katoh, E., Hanada, K., Sakita, M., Sakata, K., Nishiuchi, Y., Hirano, H.

(2003) Eur J Biochem 270: 1269-1276

Released	2003-06-17
Method	SOLUTION NMR
Organisms	Glycine max
Macromolecule	Leginsulin (protein)

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2E3M \| pdb_00002e3m	Download File View File

Crystal structure of CERT START domain

Kudo, N., Kumagai, K., Wakatsuki, S., Nishijima, M., Hanada, K., Kato, R.

(2008) Proc Natl Acad Sci U S A 105: 488-493

Released	2007-12-18
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	Lipid-transfer protein CERT (protein)

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2E3N \| pdb_00002e3n	Download File View File

Crystal structure of CERT START domain in complex with C6-ceramide (P212121)

Kudo, N., Kumagai, K., Wakatsuki, S., Nishijima, M., Hanada, K., Kato, R.

(2008) Proc Natl Acad Sci U S A 105: 488-493

Released	2007-12-18
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Homo sapiens
Macromolecule	Lipid-transfer protein CERT (protein)
Unique Ligands	6CM

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2E3O \| pdb_00002e3o	Download File View File

Crystal structure of CERT START domain in complex with C16-ceramide (P212121)

Kudo, N., Kumagai, K., Wakatsuki, S., Nishijima, M., Hanada, K., Kato, R.

(2008) Proc Natl Acad Sci U S A 105: 488-493

Released	2007-12-18
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Homo sapiens
Macromolecule	Lipid-transfer protein CERT (protein)
Unique Ligands	16C, DMS

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2E3P \| pdb_00002e3p	Download File View File

Crystal structure of CERT START domain in complex with C16-cearmide (P1)

Kudo, N., Kumagai, K., Wakatsuki, S., Nishijima, M., Hanada, K., Kato, R.

(2008) Proc Natl Acad Sci U S A 105: 488-493

Released	2007-12-18
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Homo sapiens
Macromolecule	Lipid-transfer protein CERT (protein)
Unique Ligands	16C

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2E3Q \| pdb_00002e3q	Download File View File

Crystal structure of CERT START domain in complex with C18-ceramide (P212121)

Kudo, N., Kumagai, K., Wakatsuki, S., Nishijima, M., Hanada, K., Kato, R.

(2008) Proc Natl Acad Sci U S A 105: 488-493

Released	2007-12-18
Method	X-RAY DIFFRACTION 2.08 Å
Organisms	Homo sapiens
Macromolecule	Lipid-transfer protein CERT (protein)
Unique Ligands	18C, DMS

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2E3R \| pdb_00002e3r	Download File View File

Crystal structure of CERT START domain in complex with C18-ceramide (P1)

Kudo, N., Kumagai, K., Wakatsuki, S., Nishijima, M., Hanada, K., Kato, R.

(2008) Proc Natl Acad Sci U S A 105: 488-493

Released	2007-12-18
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Homo sapiens
Macromolecule	Lipid-transfer protein CERT (protein)
Unique Ligands	18C

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2E3S \| pdb_00002e3s	Download File View File

Crystal structure of CERT START domain co-crystallized with C24-ceramide (P21)

Kudo, N., Kumagai, K., Wakatsuki, S., Nishijima, M., Hanada, K., Kato, R.

(2008) Proc Natl Acad Sci U S A 105: 488-493

Released	2007-12-18
Method	X-RAY DIFFRACTION 1.94 Å
Organisms	Homo sapiens
Macromolecule	Lipid-transfer protein CERT (protein)

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2RSG \| pdb_00002rsg	Download File View File

Solution structure of the CERT PH domain

Sugiki, T., Takeuchi, K., Tokunaga, Y., Kumagai, K., Kawano, M., Nishijima, M., Hanada, K., Takahashi, H., Shimada, I.

(2012) J Biological Chem 287: 33706-33718

Released	2012-08-15
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Collagen type IV alpha-3-binding protein (protein)

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2Z9Y \| pdb_00002z9y	Download File View File

Crystal structure of CERT START domain in complex with C10-diacylglycerol

Kudo, N., Kumagai, K., Wakatsuki, S., Nishijima, M., Hanada, K., Kato, R.

(2008) Proc Natl Acad Sci U S A 105: 488-493

Released	2008-02-12
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens
Macromolecule	Lipid-transfer protein CERT (protein)
Unique Ligands	DDR

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2Z9Z \| pdb_00002z9z	Download File View File

Crystal structure of CERT START domain(N504A mutant), in complex with C10-diacylglycerol

Kudo, N., Kumagai, K., Wakatsuki, S., Nishijima, M., Hanada, K., Kato, R.

(2008) Proc Natl Acad Sci U S A 105: 488-493

Released	2008-02-12
Method	X-RAY DIFFRACTION 1.74 Å
Organisms	Homo sapiens
Macromolecule	Lipid-transfer protein CERT (protein)
Unique Ligands	DDR

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5ZYG \| pdb_00005zyg	Download File View File

Crystal structure of CERT START domain in complex with compound B5

Suzuki, M., Nakao, N., Ueno, M., Sakai, S., Egawa, D., Hanzawa, H., Kawasaki, S., Kumagai, K., Kobayashi, S., Hanada, K.

(2019) Commun Chem

Released	2019-02-27
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens
Macromolecule	LIPID-TRANSFER PROTEIN CERT (protein)
Unique Ligands	9N3

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5ZYH \| pdb_00005zyh	Download File View File

Crystal structure of CERT START domain in complex with compound E5

Suzuki, M., Nakao, N., Ueno, M., Sakai, S., Egawa, D., Hanzawa, H., Kawasaki, S., Kumagai, K., Kobayashi, S., Hanada, K.

(2019) Commun Chem

Released	2019-02-27
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Homo sapiens
Macromolecule	LIPID-TRANSFER PROTEIN CERT (protein)
Unique Ligands	9N0

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5ZYI \| pdb_00005zyi	Download File View File

Crystal structure of CERT START domain in complex with compound E16

Suzuki, M., Nakao, N., Ueno, M., Sakai, S., Egawa, D., Hanzawa, H., Kawasaki, S., Kumagai, K., Kobayashi, S., Hanada, K.

(2019) Commun Chem

Released	2019-02-27
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	LIPID-TRANSFER PROTEIN CERT (protein)
Unique Ligands	9ML

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5ZYJ \| pdb_00005zyj	Download File View File

Crystal structure of CERT START domain in complex with compound E16A

Suzuki, M., Nakao, N., Ueno, M., Sakai, S., Egawa, D., Hanzawa, H., Kawasaki, S., Kumagai, K., Kobayashi, S., Hanada, K.

(2019) Commun Chem

Released	2019-02-27
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	LIPID-TRANSFER PROTEIN CERT (protein)
Unique Ligands	9ML, GOL

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5ZYK \| pdb_00005zyk	Download File View File

Crystal structure of CERT START domain in complex with compound E25

Suzuki, M., Nakao, N., Ueno, M., Sakai, S., Egawa, D., Hanzawa, H., Kawasaki, S., Kumagai, K., Kobayashi, S., Hanada, K.

(2019) Commun Chem

Released	2019-02-27
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Homo sapiens
Macromolecule	LIPID-TRANSFER PROTEIN CERT (protein)
Unique Ligands	9MC

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5ZYL \| pdb_00005zyl	Download File View File

Crystal structure of CERT START domain in complex with compound E25A

Suzuki, M., Nakao, N., Ueno, M., Sakai, S., Egawa, D., Hanzawa, H., Kawasaki, S., Kumagai, K., Kobayashi, S., Hanada, K.

(2019) Commun Chem

Released	2019-02-27
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens
Macromolecule	LIPID-TRANSFER PROTEIN CERT (protein)
Unique Ligands	9MC, GOL

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5ZYM \| pdb_00005zym	Download File View File

Crystal structure of CERT START domain in complex with compound E25B

Suzuki, M., Nakao, N., Ueno, M., Sakai, S., Egawa, D., Hanzawa, H., Kawasaki, S., Kumagai, K., Kobayashi, S., Hanada, K.

(2019) Commun Chem

Released	2019-02-27
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	LIPID-TRANSFER PROTEIN CERT (protein)
Unique Ligands	9M6, GOL

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6IEZ \| pdb_00006iez	Download File View File

Crystal structure of CERT START domain in complex with compound B16

Suzuki, M., Nakao, N., Ueno, M., Sakai, S., Egawa, D., Hanzawa, H., Kawasaki, S., Kumagai, K., Kobayashi, S., Hanada, K.

(2019) Commun Chem

Released	2019-02-27
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	LIPID-TRANSFER PROTEIN CERT (protein)
Unique Ligands	A50

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6IF0 \| pdb_00006if0	Download File View File

Crystal structure of CERT START domain in complex with compound D16

Suzuki, M., Nakao, N., Ueno, M., Sakai, S., Egawa, D., Hanzawa, H., Kawasaki, S., Kumagai, K., Kobayashi, S., Hanada, K.

(2019) Commun Chem

Released	2019-02-27
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens
Macromolecule	LIPID-TRANSFER PROTEIN CERT (protein)
Unique Ligands	A59

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6J0O \| pdb_00006j0o	Download File View File

Crystal structure of CERT START domain in complex with compound SC1

Suzuki, M., Nakao, N., Ueno, M., Sakai, S., Egawa, D., Hanzawa, H., Kawasaki, S., Kumagai, K., Kobayashi, S., Hanada, K.

(2019) Commun Chem

Released	2019-02-27
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens
Macromolecule	LIPID-TRANSFER PROTEIN CERT (protein)
Unique Ligands	UNX, XAF

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6J81 \| pdb_00006j81	Download File View File

Crystal structure of CERT START domain in complex with compound E14

Suzuki, M., Nakao, N., Ueno, M., Sakai, S., Egawa, D., Hanzawa, H., Kawasaki, S., Kumagai, K., Kobayashi, S., Hanada, K.

(2019) Commun Chem

Released	2019-02-27
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens
Macromolecule	LIPID-TRANSFER PROTEIN CERT (protein)
Unique Ligands	B8X

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7DPA \| pdb_00007dpa	Download File View File

Cryo-EM structure of the human ELMO1-DOCK5-Rac1 complex

Kukimoto-Niino, M., Katsura, K., Kaushik, R., Ehara, H., Yokoyama, T., Uchikubo-Kamo, T., Mishima-Tsumagari, C., Yonemochi, M., Ikeda, M., Hanada, K., Zhang, K.Y.J., Shirouzu, M.

(2021) Sci Adv 7:

Released	2021-08-04
Method	ELECTRON MICROSCOPY 3.8 Å
Organisms	Homo sapiens
Macromolecule	Dedicator of cytokinesis protein 5 (protein) Engulfment and cell motility protein 1 (protein) Ras-related C3 botulinum toxin substrate 1 (protein)

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7E3D \| pdb_00007e3d	Download File View File

Crystal structure of human acetylcholinesterase

Dileep, K.V., Ihara, K., Mishima-Tsumagari, C., Kukimoto-Niino, M., Yonemochi, M., Hanada, K., Shirouzu, M., Zhang, K.Y.J.

(2022) Int J Biol Macromol 210: 172-181

Released	2022-02-16
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Homo sapiens
Macromolecule	Acetylcholinesterase (protein)
Unique Ligands	PE8
Unique branched monosaccharides	FUC, NAG

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7E3H \| pdb_00007e3h	Download File View File

Crystal structure of human acetylcholinesterase in complex with donepezil

Dileep, K.V., Ihara, K., Mishima-Tsumagari, C., Kukimoto-Niino, M., Yonemochi, M., Hanada, K., Shirouzu, M., Zhang, K.Y.J.

(2022) Int J Biol Macromol 210: 172-181

Released	2022-02-16
Method	X-RAY DIFFRACTION 2.45 Å
Organisms	Homo sapiens
Macromolecule	Acetylcholinesterase (protein)
Unique Ligands	E20
Unique branched monosaccharides	FUC, NAG

1 to 25 of 26 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

1JU8 | pdb_00001ju8

2E3M | pdb_00002e3m

2E3N | pdb_00002e3n

2E3O | pdb_00002e3o

2E3P | pdb_00002e3p

2E3Q | pdb_00002e3q

2E3R | pdb_00002e3r

2E3S | pdb_00002e3s

2RSG | pdb_00002rsg

2Z9Y | pdb_00002z9y

2Z9Z | pdb_00002z9z

5ZYG | pdb_00005zyg

5ZYH | pdb_00005zyh

5ZYI | pdb_00005zyi

5ZYJ | pdb_00005zyj

5ZYK | pdb_00005zyk

5ZYL | pdb_00005zyl

5ZYM | pdb_00005zym

6IEZ | pdb_00006iez

6IF0 | pdb_00006if0

6J0O | pdb_00006j0o

6J81 | pdb_00006j81

7DPA | pdb_00007dpa

7E3D | pdb_00007e3d

7E3H | pdb_00007e3h