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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Yamada, Y."

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Search Summary

This query matches 40 Structures.

Refinements

Structure Determination Methodology

experimental (40)

Scientific Name of Source Organism

	Gallus gallus (8)
	Homo sapiens (6)
	Datura stramonium (5)
	Rattus norvegicus (4)
	Oryctolagus cuniculus (3)
	Synechococcus sp. (3)
	Achromobacter cycloclastes (2)
	Alcaligenes faecalis subsp. faecalis NBRC 13111 (2)
	Mus musculus (2)
	Bos taurus (1)

More...

Taxonomy

	Eukaryota (29)
	Bacteria (10)
	Archaea (1)
	Eukaryota (eukaryotes) (1)

Experimental Method

	X-RAY DIFFRACTION (33)
	ELECTRON MICROSCOPY (6)
	SOLUTION NMR (1)

Polymer Entity Type

Protein (40)

Refinement Resolution (Å)

	1.0 - 1.5 (3)
	1.5 - 2.0 (8)
	2.0 - 2.5 (12)
	2.5 - 3.0 (12)
	3.0 - 3.5 (1)
	> 4.5 (3)

Release Date

	1995 - 1999 (4)
	2000 - 2004 (8)
	2005 - 2009 (7)
	2010 - 2014 (3)
	2015 - 2019 (5)
	2020 - 2024 (12)
	2025 - 2029 (1)

Enzyme Classification Name

	Hydrolases (14)
	Oxidoreductases (8)
	Lyases (3)

Membrane Protein Annotation

OPM (1)

Symmetry Type

	Asymmetric (21)
	Cyclic (18)
	Dihedral (5)
	Helical (1)
	Octahedral (1)

SCOP Classification

	All beta proteins (10)
	Alpha and beta proteins (a/b) (9)
	All alpha proteins (6)
	Alpha and beta proteins (a+b) (5)
	Peptides (1)
	Artifacts (1)

AllSelected

1 to 25 of 40 Structures

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1AE1 \| pdb_00001ae1	Download File View File

TROPINONE REDUCTASE-I COMPLEX WITH NADP

Nakajima, K., Yamashita, A., Akama, H., Nakatsu, T., Kato, H., Hashimoto, T., Oda, J., Yamada, Y.

(1998) Proc Natl Acad Sci U S A 95: 4876-4881

Released	1998-11-18
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Datura stramonium
Macromolecule	TROPINONE REDUCTASE-I (protein)
Unique Ligands	NAP

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1AUN \| pdb_00001aun	Download File View File

PATHOGENESIS-RELATED PROTEIN 5D FROM NICOTIANA TABACUM

Koiwa, H., Kato, H., Nakatsu, T., Oda, J., Yamada, Y., Sato, F.

(1999) J Mol Biology 286: 1137-1145

Released	1998-03-04
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Nicotiana tabacum
Macromolecule	PR-5D (protein)

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1IPE \| pdb_00001ipe	Download File View File

TROPINONE REDUCTASE-II COMPLEXED WITH NADPH

Yamashita, A., Endo, M., Higashi, T., Nakatsu, T., Yamada, Y., Oda, J., Kato, H., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2003) Biochemistry 42: 5566-5573

Released	2003-06-03
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Datura stramonium
Macromolecule	TROPINONE REDUCTASE-II (protein)
Unique Ligands	NDP

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1IPF \| pdb_00001ipf	Download File View File

TROPINONE REDUCTASE-II COMPLEXED WITH NADPH AND TROPINONE

Yamashita, A., Endo, M., Higashi, T., Nakatsu, T., Yamada, Y., Oda, J., Kato, H., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2003) Biochemistry 42: 5566-5573

Released	2003-06-03
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Datura stramonium
Macromolecule	TROPINONE REDUCTASE-II (protein)
Unique Ligands	NDP, TNE

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1ITK \| pdb_00001itk	Download File View File

Crystal structure of catalase-peroxidase from Haloarcula marismortui

Yamada, Y., Fujiwara, T., Sato, T., Igarashi, N., Tanaka, N.

(2002) Nat Struct Biol 9: 691-695

Released	2002-08-28
Method	X-RAY DIFFRACTION 2 Å
Organisms	Haloarcula marismortui
Macromolecule	catalase-peroxidase (protein)
Unique Ligands	CL, HEM, SO4, UNX

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1VYT \| pdb_00001vyt	Download File View File

beta3 subunit complexed with aid

Chen, Y.-H., Li, M.-H., Zhang, Y., He, L.-L., Yamada, Y., Fitzmaurice, A., Yang, S., Zhang, H., Tong, L., Yang, J.

(2004) Nature 429: 675

Released	2004-06-15
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Rattus norvegicus
Macromolecule	CALCIUM CHANNEL BETA-3 SUBUNIT (protein) VOLTAGE-DEPENDENT L-TYPE CALCIUM CHANNEL ALPHA-1C SUBUNIT (protein)

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1VYU \| pdb_00001vyu	Download File View File

Beta3 subunit of Voltage-gated Ca2+-channel

Chen, Y.-H., Li, M.-H., Zhang, Y., He, L.-L., Yamada, Y., Fitzmaurice, A., Yang, S., Zhang, H., Liang, T., Yang, J.

(2004) Nature 429: 675

Released	2004-06-15
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Rattus norvegicus
Macromolecule	CALCIUM CHANNEL BETA-3 SUBUNIT (protein)

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1VYV \| pdb_00001vyv	Download File View File

beta4 subunit of Ca2+ channel

Chen, Y.-H., Li, M.-H., Zhang, Y., He, L.-L., Yamada, Y., Fitzmaurice, A., Yang, S., Zhang, H., Liang, T., Yang, J.

(2004) Nature 429: 675

Released	2004-06-15
Method	X-RAY DIFFRACTION 3 Å
Organisms	Rattus norvegicus
Macromolecule	CALCIUM CHANNEL BETA-4SUBUNIT (protein)

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1WTM \| pdb_00001wtm	Download File View File

X-ray structure of HEW Lysozyme Orthorhombic Crystal formed in the Earth's magnetic field

Saijo, S., Yamada, Y., Sato, T., Tanaka, N., Matsui, T., Sazaki, G., Nakajima, K., Matsuura, Y.

(2005) Acta Crystallogr D Biol Crystallogr 61: 207-217

Released	2004-12-14
Method	X-RAY DIFFRACTION 1.33 Å
Organisms	Gallus gallus
Macromolecule	Lysozyme C (protein)
Unique Ligands	CL

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1WTN \| pdb_00001wtn	Download File View File

The structure of HEW Lysozyme Orthorhombic Crystal Growth under a High Magnetic Field

Saijo, S., Yamada, Y., Sato, T., Tanaka, N., Matsui, T., Sazaki, G., Nakajima, K., Matsuura, Y.

(2005) Acta Crystallogr D Biol Crystallogr 61: 207-217

Released	2004-12-14
Method	X-RAY DIFFRACTION 1.13 Å
Organisms	Gallus gallus
Macromolecule	Lysozyme C (protein)
Unique Ligands	CL

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2AE1 \| pdb_00002ae1	Download File View File

TROPINONE REDUCTASE-II

Nakajima, K., Yamashita, A., Akama, H., Nakatsu, T., Kato, H., Hashimoto, T., Oda, J., Yamada, Y.

(1998) Proc Natl Acad Sci U S A 95: 4876-4881

Released	1998-11-18
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Datura stramonium
Macromolecule	TROPINONE REDUCTASE-II (protein)

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2AE2 \| pdb_00002ae2	Download File View File

TROPINONE REDUCTASE-II COMPLEXED WITH NADP+ AND PSEUDOTROPINE

Yamashita, A., Kato, H., Wakatsuki, S., Tomizaki, T., Nakatsu, T., Nakajima, K., Hashimoto, T., Yamada, Y., Oda, J.

(1999) Biochemistry 38: 7630-7637

Released	1999-02-02
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Datura stramonium
Macromolecule	PROTEIN (TROPINONE REDUCTASE-II) (protein)
Unique Ligands	NAP, PTO

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2DWX \| pdb_00002dwx	Download File View File

Co-crystal Structure Analysis of GGA1-GAE with the WNSF motif

Inoue, M., Shiba, T., Yamada, Y., Ihara, K., Kawasaki, M., Kato, R., Nakayama, K., Wakatsuki, S.

(2007) Traffic 8: 904-913

Released	2007-04-17
Method	X-RAY DIFFRACTION 2.55 Å
Organisms	Homo sapiens
Macromolecule	ADP-ribosylation factor-binding protein GGA1 (protein) hinge peptide from ADP-ribosylation factor binding protein GGA1 (protein)

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2DWY \| pdb_00002dwy	Download File View File

Crystal Structure Analysis of GGA1-GAE

Inoue, M., Shiba, T., Yamada, Y., Ihara, K., Kawasaki, M., Kato, R., Nakayama, K., Wakatsuki, S.

(2007) Traffic 8: 904-913

Released	2007-04-17
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA1 (protein)

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2DYT \| pdb_00002dyt	Download File View File

The crystal structure of Saccharomyces cerevisiae Atg3

Yamada, Y., Suzuki, N.N., Inagaki, F.

(2007) J Biological Chem 282: 8036-8043

Released	2007-01-23
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Autophagy-related protein 3 (protein)
Unique Ligands	SO4

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2Z44 \| pdb_00002z44	Download File View File

Crystal Structure of Selenomethionine-labeled ORF134

Tomimoto, Y., Ihara, K., Onizuka, T., Kanai, S., Ashida, H., Yokota, A., Tanaka, S., Miyasaka, H., Yamada, Y., Kato, R., Wakatsuki, S.

To be published

Released	2008-06-24
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Synechococcus sp.
Macromolecule	ORF134 (protein)

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2Z45 \| pdb_00002z45	Download File View File

Crystal Structure of Zn-bound ORF134

Tomimoto, Y., Ihara, K., Onizuka, T., Kanai, S., Ashida, H., Yokota, A., Tanaka, S., Miyasaka, H., Yamada, Y., Kato, R., Wakatsuki, S.

To be published

Released	2008-06-24
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Synechococcus sp.
Macromolecule	ORF134 (protein)
Unique Ligands	ZN

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2Z46 \| pdb_00002z46	Download File View File

Crystal Structure of Native-ORF134

Tomimoto, Y., Ihara, K., Onizuka, T., Kanai, S., Ashida, H., Yokota, A., Tanaka, S., Miyasaka, H., Yamada, Y., Kato, R., Wakatsuki, S.

To be published

Released	2008-06-24
Method	X-RAY DIFFRACTION 2.97 Å
Organisms	Synechococcus sp.
Macromolecule	ORF134 (protein)

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3H7G \| pdb_00003h7g	Download File View File

Apo-FR with AU ions

Abe, M., Ueno, T., Abe, S., Suzuki, M., Goto, T., Toda, Y., Akita, T., Yamada, Y., Watanabe, Y.

(2009) Chem Commun (Camb) 32: 4871-4873

Released	2009-09-15
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Equus caballus
Macromolecule	Ferritin light chain (protein)
Unique Ligands	AU3, CD, GOL, SO4

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3J82 \| pdb_00003j82	Download File View File

Electron cryo-microscopy of DNGR-1 in complex with F-actin

Hanc, P., Fujii, T., Yamada, Y., Huotari, J., Schulz, O., Ahrens, S., Kjaer, S., Way, M., Namba, K., Reis e Sousa, C.

(2015) Immunity 42: 839-849

Released	2015-05-20
Method	ELECTRON MICROSCOPY 7.7 Å
Organisms	Homo sapiens Mus musculus
Macromolecule	Actin, cytoplasmic 1 (protein) C-type lectin domain family 9 member A (protein)
Unique Ligands	ADP, CA

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3VV1 \| pdb_00003vv1	Download File View File

Crystal Structure of Caenorhabditis elegans galectin LEC-6

Makyio, H., Takeuchi, T., Tamura, M., Nishiyama, K., Takahashi, H., Natsugari, H., Arata, Y., Kasai, K., Yamada, Y., Wakatsuki, S., Kato, R.

(2013) Glycobiology 23: 797-805

Released	2013-05-22
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Caenorhabditis elegans
Macromolecule	Protein LEC-6 (protein)
Unique Ligands	MG
Unique branched monosaccharides	FUC, GAL