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234,785 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Yamada, M."

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Search Summary

This query matches 68 Structures.

Refinements

Structure Determination Methodology

experimental (68)

Scientific Name of Source Organism

	Homo sapiens (16)
	Streptococcus pneumoniae (8)
	Chromohalobacter sp. 560 (7)
	Streptomyces griseolus (5)
	Sus scrofa (5)
	Pseudomonas cichorii (4)
	Thermoactinomyces vulgaris (4)
	Stutzerimonas stutzeri (3)
	Campylobacter jejuni (2)
	Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 (2)

More...

Taxonomy

	Bacteria (40)
	Eukaryota (23)
	Archaea (5)
	Eukaryota (eukaryotes) (2)
	other sequences (2)
	unclassified sequences (1)

Experimental Method

X-RAY DIFFRACTION (68)

Polymer Entity Type

	Protein (68)
	DNA (2)
	RNA (2)

Refinement Resolution (Å)

	1.0 - 1.5 (1)
	1.5 - 2.0 (24)
	2.0 - 2.5 (21)
	2.5 - 3.0 (17)
	3.0 - 3.5 (5)

Release Date

	1990 - 1994 (1)
	2000 - 2004 (3)
	2005 - 2009 (40)
	2010 - 2014 (8)
	2015 - 2019 (12)
	2020 - 2024 (4)

Enzyme Classification Name

	Hydrolases (21)
	Oxidoreductases (13)
	Isomerases (7)
	Transferases (4)
	Lyases (1)

Symmetry Type

	Asymmetric (44)
	Cyclic (20)
	Dihedral (6)
	Helical (1)

SCOP Classification

	Alpha and beta proteins (a+b) (17)
	Multi-domain proteins (alpha and beta) (15)
	All alpha proteins (8)
	All beta proteins (13)
	Alpha and beta proteins (a/b) (10)
	Artifacts (5)

AllSelected

1 to 25 of 68 Structures

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1WD8 \| pdb_00001wd8	Download File View File

Calcium free form of human peptidylarginine deiminase type4 (PAD4)

Arita, K., Hashimoto, H., Shimizu, T., Nakashima, K., Yamada, M., Sato, M.

(2004) Nat Struct Mol Biol 11: 777-783

Released	2004-07-13
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Homo sapiens
Macromolecule	Protein-arginine deiminase type IV (protein)

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1WD9 \| pdb_00001wd9	Download File View File

Calcium bound form of human peptidylarginine deiminase type4 (PAD4)

Arita, K., Hashimoto, H., Shimizu, T., Nakashima, K., Yamada, M., Sato, M.

(2004) Nat Struct Mol Biol 11: 777-783

Released	2004-07-13
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Homo sapiens
Macromolecule	Protein-arginine deiminase type IV (protein)
Unique Ligands	CA, SO4

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1WDA \| pdb_00001wda	Download File View File

Crystal structure of human peptidylarginine deiminase type4 (PAD4) in complex with benzoyl-L-arginine amide

Arita, K., Hashimoto, H., Shimizu, T., Nakashima, K., Yamada, M., Sato, M.

(2004) Nat Struct Mol Biol 11: 777-783

Released	2004-07-13
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	Protein-arginine deiminase type IV (protein)
Unique Ligands	BAG, CA, SO4

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1WY9 \| pdb_00001wy9	Download File View File

Crystal structure of microglia-specific protein, Iba1

Yamada, M., Imai, Y., Kohsaka, S., Kamitori, S.

(2006) J Mol Biology 364: 449-457

Released	2006-02-21
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Mus musculus
Macromolecule	Allograft inflammatory factor 1 (protein)
Unique Ligands	CA

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1ZZE \| pdb_00001zze	Download File View File

X-ray Structure of NADPH-dependent Carbonyl Reductase from Sporobolomyces salmonicolor

Kamitori, S., Iguchi, A., Ohtaki, A., Yamada, M., Kita, K.

(2005) J Mol Biology 352: 551-558

Released	2005-09-06
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Sporobolomyces salmonicolor
Macromolecule	Aldehyde reductase II (protein)
Unique Ligands	SO4

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2DEW \| pdb_00002dew	Download File View File

Crystal structure of human peptidylarginine deiminase 4 in complex with histone H3 N-terminal tail including Arg8

Arita, K., Shimizu, T., Hashimoto, H., Hidaka, Y., Yamada, M., Sato, M.

(2006) Proc Natl Acad Sci U S A 103: 5291-5296

Released	2006-04-11
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	10-mer peptide from histone H3 (protein) Protein-arginine deiminase type IV (protein)
Unique Ligands	CA, SO4

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2DEX \| pdb_00002dex	Download File View File

Crystal structure of human peptidylarginine deiminase 4 in complex with histone H3 N-terminal peptide including Arg17

Arita, K., Shimizu, T., Hashimoto, H., Hidaka, Y., Yamada, M., Sato, M.

(2006) Proc Natl Acad Sci U S A 103: 5291-5296

Released	2006-04-11
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	10-mer peptide from histone H3 (protein) Protein-arginine deiminase type IV (protein)
Unique Ligands	CA, SO4

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2DEY \| pdb_00002dey	Download File View File

Crystal structure of human peptidylarginine deiminase 4 in complex with histone H4 N-terminal tail including Arg3

Arita, K., Shimizu, T., Hashimoto, H., Hidaka, Y., Yamada, M., Sato, M.

(2006) Proc Natl Acad Sci U S A 103: 5291-5296

Released	2006-04-11
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Homo sapiens
Macromolecule	10-mer peptide from histone H4 (protein) Protein-arginine deiminase type IV (protein)
Unique Ligands	CA, SO4

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2E6X \| pdb_00002e6x	Download File View File

X-ray structure of TT1592 from Thermus thermophilus HB8

Yamada, M., Nakagawa, N., Kanagawa, M., Kuramitsu, S., Kamitori, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2007-12-18
Method	X-RAY DIFFRACTION 2 Å
Organisms	Thermus thermophilus HB8
Macromolecule	Hypothetical protein TTHA1281 (protein)

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2ECE \| pdb_00002ece	Download File View File

X-ray structure of hypothetical selenium-binding protein from Sulfolobus tokodaii, ST0059

Yamada, M., Yoshida, H., Kuramitsu, S., Kamitori, S.

To be published

Released	2008-01-01
Method	X-RAY DIFFRACTION 2 Å
Organisms	Sulfurisphaera tokodaii
Macromolecule	462aa long hypothetical selenium-binding protein (protein)

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2HCV \| pdb_00002hcv	Download File View File

Crystal structure of L-rhamnose isomerase from Pseudomonas stutzeri with metal ion

Yoshida, H., Yamada, M., Takada, G., Izumori, K., Kamitori, S.

(2007) J Mol Biology 365: 1505-1516

Released	2006-12-19
Method	X-RAY DIFFRACTION 2 Å
Organisms	Stutzerimonas stutzeri
Macromolecule	L-rhamnose isomerase (protein)
Unique Ligands	ZN

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2I56 \| pdb_00002i56	Download File View File

Crystal structure of L-Rhamnose Isomerase from Pseudomonas stutzeri with L-Rhamnose

Yoshida, H., Yamada, M., Takada, G., Izumori, K., Kamitori, S.

(2007) J Mol Biology 365: 1505-1516

Released	2006-12-19
Method	X-RAY DIFFRACTION 1.97 Å
Organisms	Stutzerimonas stutzeri
Macromolecule	L-rhamnose isomerase (protein)
Unique Ligands	RNS, ZN

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2I57 \| pdb_00002i57	Download File View File

Crystal Structure of L-Rhamnose Isomerase from Pseudomonas stutzeri in Complex with D-Allose

Yoshida, H., Yamada, M., Takada, G., Izumori, K., Kamitori, S.

(2007) J Mol Biology 365: 1505-1516

Released	2006-12-19
Method	X-RAY DIFFRACTION 1.97 Å
Organisms	Stutzerimonas stutzeri
Macromolecule	L-rhamnose isomerase (protein)
Unique Ligands	AOS, ZN

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2OHD \| pdb_00002ohd	Download File View File

Crystal structure of hypothetical molybdenum cofactor biosynthesis protein C from Sulfolobus tokodaii

Yoshida, H., Yamada, M., Kuramitsu, S., Kamitori, S.

(2008) Acta Crystallogr Sect F Struct Biol Cryst Commun 64: 589-592

Released	2007-11-27
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Sulfurisphaera tokodaii str. 7
Macromolecule	Probable molybdenum cofactor biosynthesis protein C (protein)

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2OU4 \| pdb_00002ou4	Download File View File

Crystal structure of D-tagatose 3-epimerase from Pseudomonas cichorii

Yoshida, H., Yamada, M., Nishitani, T., Takada, G., Izumori, K., Kamitori, S.

(2007) J Mol Biology 374: 443-453

Released	2007-12-25
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Pseudomonas cichorii
Macromolecule	D-tagatose 3-epimerase (protein)
Unique Ligands	MN

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2QUL \| pdb_00002qul	Download File View File

Crystal structure of D-tagatose 3-epimerase from Pseudomonas cichorii at 1.79 A resolution

Yoshida, H., Yamada, M., Nishitani, T., Takada, G., Izumori, K., Kamitori, S.

(2007) J Mol Biology 374: 443-453

Released	2007-12-25
Method	X-RAY DIFFRACTION 1.79 Å
Organisms	Pseudomonas cichorii
Macromolecule	D-tagatose 3-epimerase (protein)
Unique Ligands	MN

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2QUM \| pdb_00002qum	Download File View File

Crystal structure of D-tagatose 3-epimerase from Pseudomonas cichorii with D-tagatose

Yoshida, H., Yamada, M., Nishitani, T., Takada, G., Izumori, K., Kamitori, S.

(2007) J Mol Biology 374: 443-453

Released	2007-12-25
Method	X-RAY DIFFRACTION 2.28 Å
Organisms	Pseudomonas cichorii
Macromolecule	D-tagatose 3-epimerase (protein)
Unique Ligands	MN, TAG

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2QUN \| pdb_00002qun	Download File View File

Crystal Structure of D-tagatose 3-epimerase from Pseudomonas cichorii in Complex with D-fructose

Yoshida, H., Yamada, M., Nishitani, T., Takada, G., Izumori, K., Kamitori, S.

(2007) J Mol Biology 374: 443-453

Released	2007-12-25
Method	X-RAY DIFFRACTION 2.06 Å
Organisms	Pseudomonas cichorii
Macromolecule	D-tagatose 3-epimerase (protein)
Unique Ligands	FUD, MN

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2Z2L \| pdb_00002z2l	Download File View File

Penicillin-Binding Protein 2X (PBP2X) from Streptococcus pneumoniae

Yamada, M., Watanabe, T., Takeuchi, Y.

(2007) Antimicrob Agents Chemother 51: 3902-3907

Released	2007-09-04
Method	X-RAY DIFFRACTION 2.85 Å
Organisms	Streptococcus pneumoniae
Macromolecule	Penicillin-binding protein 2X (protein)
Unique Ligands	SO4

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2Z2M \| pdb_00002z2m	Download File View File

Cefditoren-Acylated Penicillin-Binding Protein 2X (PBP2X) from Streptococcus pneumoniae

Yamada, M., Watanabe, T., Takeuchi, Y.

(2007) Antimicrob Agents Chemother 51: 3902-3907

Released	2007-09-04
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Streptococcus pneumoniae
Macromolecule	Penicillin-binding protein 2X (protein)
Unique Ligands	CDS, SO4

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2Z4P \| pdb_00002z4p	Download File View File

Crystal structure of FFRP-DM1

Yamada, M., Koike, H., Kudo, N., Suzuki, M.

(2007) Structure 15: 1325-1338

Released	2007-09-18
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Pyrococcus horikoshii OT3
Macromolecule	75aa long hypothetical regulatory protein AsnC (protein)
Unique Ligands	ILE

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2Z5J \| pdb_00002z5j	Download File View File

Free Transportin 1

Imasaki, T., Shimizu, T., Hashimoto, H., Hidaka, Y., Yamada, M., Sato, M.

(2007) Mol Cell 28: 57-67

Released	2007-10-23
Method	X-RAY DIFFRACTION 3.4 Å
Organisms	Homo sapiens
Macromolecule	Transportin-1 (protein)

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2Z5K \| pdb_00002z5k	Download File View File

Complex of Transportin 1 with TAP NLS

Imasaki, T., Shimizu, T., Hashimoto, H., Hidaka, Y., Yamada, M., Kose, S., Imamoto, N., Sato, M.

(2007) Mol Cell 28: 57-67

Released	2007-10-23
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Homo sapiens
Macromolecule	Nuclear RNA export factor 1 (protein) Transportin-1 (protein)
Unique Ligands	PO4

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2Z5M \| pdb_00002z5m	Download File View File

Complex of Transportin 1 with TAP NLS, crystal form 2

Imasaki, T., Shimizu, T., Hashimoto, H., Hidaka, Y., Kose, S., Imamoto, N., Yamada, M., Sato, M.

(2007) Mol Cell 28: 57-67

Released	2007-10-23
Method	X-RAY DIFFRACTION 3 Å
Organisms	Homo sapiens
Macromolecule	Nuclear RNA export factor 1 (protein) Transportin-1 (protein)

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2Z5N \| pdb_00002z5n	Download File View File

Complex of Transportin 1 with hnRNP D NLS

Imasaki, T., Shimizu, T., Hashimoto, H., Hidaka, Y., Kose, S., Imamoto, N., Yamada, M., Sato, M.

(2007) Mol Cell 28: 57-67

Released	2007-10-23
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Homo sapiens
Macromolecule	Heterogeneous nuclear ribonucleoprotein D0 (protein) Transportin-1 (protein)

1 to 25 of 68 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

Symmetry Type

SCOP Classification

1WD8 | pdb_00001wd8

1WD9 | pdb_00001wd9

1WDA | pdb_00001wda

1WY9 | pdb_00001wy9

1ZZE | pdb_00001zze

2DEW | pdb_00002dew

2DEX | pdb_00002dex

2DEY | pdb_00002dey

2E6X | pdb_00002e6x

2ECE | pdb_00002ece

2HCV | pdb_00002hcv

2I56 | pdb_00002i56

2I57 | pdb_00002i57

2OHD | pdb_00002ohd

2OU4 | pdb_00002ou4

2QUL | pdb_00002qul

2QUM | pdb_00002qum

2QUN | pdb_00002qun

2Z2L | pdb_00002z2l

2Z2M | pdb_00002z2m

2Z4P | pdb_00002z4p

2Z5J | pdb_00002z5j

2Z5K | pdb_00002z5k

2Z5M | pdb_00002z5m

2Z5N | pdb_00002z5n