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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Yamada, Y."

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Search Summary

This query matches 83 Structures.

Refinements

Structure Determination Methodology

experimental (83)

Scientific Name of Source Organism

	Mus musculus (11)
	Pseudomonas aeruginosa PAO1 (11)
	Homo sapiens (9)
	Gallus gallus (8)
	Saccharomyces cerevisiae (8)
	Datura stramonium (5)
	Oryctolagus cuniculus (5)
	Bifidobacterium bifidum (4)
	Rattus norvegicus (4)
	Escherichia coli (3)

More...

Taxonomy

	Eukaryota (50)
	Bacteria (30)
	Archaea (3)
	Eukaryota (eukaryotes) (1)

Experimental Method

	X-RAY DIFFRACTION (72)
	ELECTRON MICROSCOPY (9)
	SOLUTION NMR (2)

Polymer Entity Type

	Protein (82)
	DNA (2)
	RNA (1)

Refinement Resolution (Å)

	1.0 - 1.5 (7)
	1.5 - 2.0 (21)
	2.0 - 2.5 (22)
	2.5 - 3.0 (23)
	3.0 - 3.5 (2)
	3.5 - 4.0 (1)
	> 4.5 (5)

Release Date

	1995 - 1999 (7)
	2000 - 2004 (11)
	2005 - 2009 (22)
	2010 - 2014 (5)
	2015 - 2019 (10)
	2020 - 2024 (27)
	2025 - 2029 (1)

Enzyme Classification Name

	Hydrolases (36)
	Oxidoreductases (8)
	Lyases (3)
	Transferases (1)

Membrane Protein Annotation

	OPM (2)
	MemProtMD (1)
	PDBTM (1)
	mpstruc (1)

Symmetry Type

	Asymmetric (56)
	Cyclic (26)
	Dihedral (7)
	Helical (2)
	Octahedral (1)

SCOP Classification

	All beta proteins (20)
	Alpha and beta proteins (a/b) (12)
	Alpha and beta proteins (a+b) (8)
	All alpha proteins (6)
	Artifacts (3)
	Peptides (1)
	Small proteins (2)

AllSelected

1 to 25 of 83 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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1DYK \| pdb_00001dyk	Download File View File

Laminin alpha 2 chain LG4-5 domain pair

Tisi, D., Talts, J.F., Timple, R., Hohenester, E.

(2000) EMBO J 19: 1432

Released	2001-02-04
Method	X-RAY DIFFRACTION 2 Å
Organisms	Mus musculus
Macromolecule	LAMININ ALPHA 2 CHAIN (protein)
Unique Ligands	CA

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1ERZ \| pdb_00001erz	Download File View File

CRYSTAL STRUCTURE OF N-CARBAMYL-D-AMINO ACID AMIDOHYDROLASE WITH A NOVEL CATALYTIC FRAMEWORK COMMON TO AMIDOHYDROLASES

Nakai, T., Hasegawa, T., Yamashita, E., Yamamoto, M., Kumasaka, T., Ueki, T., Nanba, H., Ikenaka, Y., Takahashi, S., Sato, M., Tsukihara, T.

(2000) Structure 8: 729-737

Released	2001-04-06
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Agrobacterium sp. KNK712
Macromolecule	N-CARBAMYL-D-AMINO ACID AMIDOHYDROLASE (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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1KLO \| pdb_00001klo	Download File View File

CRYSTAL STRUCTURE OF THREE CONSECUTIVE LAMININ-TYPE EPIDERMAL GROWTH FACTOR-LIKE (LE) MODULES OF LAMININ GAMMA1 CHAIN HARBORING THE NIDOGEN BINDING SITE

Stetefeld, J., Mayer, U., Timpl, R., Huber, R.

(1996) J Mol Biology 257: 644-657

Released	1997-08-20
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Mus musculus
Macromolecule	LAMININ (protein)

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1OKQ \| pdb_00001okq	Download File View File

LAMININ ALPHA 2 CHAIN LG4-5 DOMAIN PAIR, CA1 SITE MUTANT

Wizemann, H., Garbe, J.H.O., Friedrich, M.V.K., Timpl, R., Sasaki, T., Hohenester, E.

(2003) J Mol Biology 332: 635

Released	2003-09-11
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Mus musculus
Macromolecule	LAMININ ALPHA 2 CHAIN (protein)
Unique Ligands	CA

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1QU0 \| pdb_00001qu0	Download File View File

CRYSTAL STRUCTURE OF THE FIFTH LAMININ G-LIKE MODULE OF THE MOUSE LAMININ ALPHA2 CHAIN

Hohenester, E., Tisi, D., Talts, J.F., Timpl, R.

(1999) Mol Cell 4: 783-792

Released	1999-12-03
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	Mus musculus
Macromolecule	LAMININ ALPHA2 CHAIN (protein)
Unique Ligands	CA, SO4

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1TLE \| pdb_00001tle	Download File View File

LE (LAMININ-TYPE EGF-LIKE) MODULE GIII4 IN SOLUTION AT PH 3.5 AND 290 K, NMR, 14 STRUCTURES

Baumgartner, R., Czisch, M., Mayer, U., Schl, E.P., Huber, R., Timpl, R., Holak, T.A.

(1996) J Mol Biology 257: 658-668

Released	1997-02-12
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	LAMININ (protein)

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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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2A6V \| pdb_00002a6v	Download File View File

Crystal structure of Emp46p carbohydrate recognition domain (CRD), potassium-bound form

Satoh, T., Sato, K., Kanoh, A., Yamashita, K., Kato, R., Nakano, A., Wakatsuki, S.

(2006) J Biological Chem 281: 10410-10419

Released	2006-01-31
Method	X-RAY DIFFRACTION 1.52 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Emp46p (protein)
Unique Ligands	EDO, K

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2A6W \| pdb_00002a6w	Download File View File

Crystal structure of Emp46p carbohydrate recognition domain (CRD), metal-free form

Satoh, T., Sato, K., Kanoh, A., Yamashita, K., Kato, R., Nakano, A., Wakatsuki, S.

(2006) J Biological Chem 281: 10410-10419

Released	2006-01-31
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Emp46p (protein)

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2A6X \| pdb_00002a6x	Download File View File

Crystal structure of Emp46p carbohydrate recognition domain (CRD), Y131F mutant

Satoh, T., Sato, K., Kanoh, A., Yamashita, K., Kato, R., Nakano, A., Wakatsuki, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2006) J Biological Chem 281: 10410-10419

Released	2006-01-31
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Emp46p (protein)
Unique Ligands	EDO, K

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2A6Y \| pdb_00002a6y	Download File View File

Crystal structure of Emp47p carbohydrate recognition domain (CRD), tetragonal crystal form

Satoh, T., Sato, K., Kanoh, A., Yamashita, K., Kato, R., Nakano, A., Wakatsuki, S.

(2006) J Biological Chem 281: 10410-10419

Released	2006-01-31
Method	X-RAY DIFFRACTION 1.42 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Emp47p (form1) (protein)
Unique Ligands	SO4

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2A6Z \| pdb_00002a6z	Download File View File

Crystal structure of Emp47p carbohydrate recognition domain (CRD), monoclinic crystal form 1

Satoh, T., Sato, K., Kanoh, A., Yamashita, K., Kato, R., Nakano, A., Wakatsuki, S.

(2006) J Biological Chem 281: 10410-10419

Released	2006-01-31
Method	X-RAY DIFFRACTION 1 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Emp47p (form2) (protein)

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2A70 \| pdb_00002a70	Download File View File

Crystal structure of Emp47p carbohydrate recognition domain (CRD), monoclinic crystal form 2

Satoh, T., Sato, K., Kanoh, A., Yamashita, K., Katoh, R., Nakano, A., Wakatsuki, S.

(2006) J Biological Chem 281: 10410-10419

Released	2006-01-31
Method	X-RAY DIFFRACTION 1.1 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Emp47p (protein)
Unique Ligands	EDO

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2A71 \| pdb_00002a71	Download File View File

Crystal structure of Emp47p carbohydrate recognition domain (CRD), orthorhombic crystal form

Satoh, T., Sato, K., Kanoh, A., Yamashita, K., Kato, R., Nakano, A., Wakatsuki, S.

(2006) J Biological Chem 281: 10410-10419

Released	2006-01-31
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Emp47p (protein)

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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

1 to 25 of 83 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

1AE1 | pdb_00001ae1

1AUN | pdb_00001aun

1DYK | pdb_00001dyk

1ERZ | pdb_00001erz

1IPE | pdb_00001ipe

1IPF | pdb_00001ipf

1ITK | pdb_00001itk

1KLO | pdb_00001klo

1OKQ | pdb_00001okq

1QU0 | pdb_00001qu0

1TLE | pdb_00001tle

1VYT | pdb_00001vyt

1VYU | pdb_00001vyu

1VYV | pdb_00001vyv

1WTM | pdb_00001wtm

1WTN | pdb_00001wtn

2A6V | pdb_00002a6v

2A6W | pdb_00002a6w

2A6X | pdb_00002a6x

2A6Y | pdb_00002a6y

2A6Z | pdb_00002a6z

2A70 | pdb_00002a70

2A71 | pdb_00002a71

2AE1 | pdb_00002ae1

2AE2 | pdb_00002ae2