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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Yamaguchi, Y."

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Search Summary

This query matches 80 Structures.

Refinements

Structure Determination Methodology

experimental (80)

Scientific Name of Source Organism

	Homo sapiens (31)
	Mus musculus (13)
	Serratia marcescens (8)
	Bos taurus (5)
	Mycothermus thermophilus (4)
	Phaseolus vulgaris (4)
	Calystegia sepium (2)
	Escherichia coli (2)
	Plodia interpunctella (2)
	Rattus norvegicus (2)

More...

Taxonomy

	Eukaryota (67)
	Bacteria (13)

Experimental Method

	X-RAY DIFFRACTION (71)
	SOLUTION NMR (9)

Polymer Entity Type

Protein (80)

Refinement Resolution (Å)

	1.5 - 2.0 (27)
	2.0 - 2.5 (30)
	2.5 - 3.0 (11)
	3.0 - 3.5 (3)

Release Date

	2000 - 2004 (3)
	2005 - 2009 (21)
	2010 - 2014 (35)
	2015 - 2019 (17)
	2020 - 2024 (4)

Enzyme Classification Name

	Hydrolases (15)
	Transferases (6)
	Translocases (3)
	Oxidoreductases (5)
	Isomerases (4)
	Ligases (4)
	Lyases (1)

Membrane Protein Annotation

	MemProtMD (3)
	PDBTM (3)
	OPM (1)

Symmetry Type

	Asymmetric (60)
	Cyclic (20)
	Dihedral (4)
	Octahedral (1)

SCOP Classification

	Alpha and beta proteins (a+b) (25)
	Membrane and cell surface proteins and peptides (3)
	All beta proteins (17)
	Artifacts (17)
	All alpha proteins (5)
	Alpha and beta proteins (a/b) (5)
	Small proteins (3)
	Multi-domain proteins (alpha and beta) (1)

AllSelected

1 to 25 of 80 Structures

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1IYF \| pdb_00001iyf	Download File View File

Solution structure of ubiquitin-like domain of human parkin

Sakata, E., Yamaguchi, Y., Kurimoto, E., Kikuchi, J., Yokoyama, S., Kawahara, H., Yokosawa, H., Hattori, N., Mizuno, Y., Tanaka, K., Kato, K., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2003) EMBO Rep 4: 301-306

Released	2003-03-25
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	parkin (protein)

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1UMH \| pdb_00001umh	Download File View File

Structural basis of sugar-recognizing ubiquitin ligase

Mizushima, T., Hirao, T., Yoshida, Y., Lee, S.J., Chiba, T., Iwai, K., Yamaguchi, Y., Kato, K., Tsukihara, T., Tanaka, K., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2004) Nat Struct Mol Biol 11: 365-370

Released	2004-04-06
Method	X-RAY DIFFRACTION 2 Å
Organisms	Mus musculus
Macromolecule	F-box only protein 2 (protein)
Unique Ligands	NI

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1UMI \| pdb_00001umi	Download File View File

Structural basis of sugar-recognizing ubiquitin ligase

Mizushima, T., Hirao, T., Yoshida, Y., Lee, S.J., Chiba, T., Iwai, K., Yamaguchi, Y., Kato, K., Tsukihara, T., Tanaka, K.

(2004) Nat Struct Mol Biol 11: 365-370

Released	2004-04-06
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Mus musculus
Macromolecule	F-box only protein 2 (protein)
Unique branched monosaccharides	NAG, NDG

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1VGN \| pdb_00001vgn	Download File View File

Structure-based design of the irreversible inhibitors to metallo--lactamase (IMP-1)

Kurosaki, H., Yamaguchi, Y., Higashi, T., Soga, K., Matsueda, S., Misumi, S., Yamagata, Y., Arakawa, Y., Goto, M.

(2005) Angew Chem Int Ed Engl 44: 3861-3864

Released	2005-06-21
Method	X-RAY DIFFRACTION 2.63 Å
Organisms	Serratia marcescens
Macromolecule	Beta-lactamase IMP-1 (protein)
Unique Ligands	ACY, OPS, ZN

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1WR6 \| pdb_00001wr6	Download File View File

Crystal structure of GGA3 GAT domain in complex with ubiquitin

Kawasaki, M., Shiba, T., Shiba, Y., Yamaguchi, Y., Matsugaki, N., Igarashi, N., Suzuki, M., Kato, R., Kato, K., Nakayama, K., Wakatsuki, S.

(2005) Genes Cells 10: 639-654

Released	2005-06-28
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Bos taurus Homo sapiens
Macromolecule	ADP-ribosylation factor binding protein GGA3 (protein) ubiquitin (protein)

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1WRD \| pdb_00001wrd	Download File View File

Crystal structure of Tom1 GAT domain in complex with ubiquitin

Akutsu, M., Kawasaki, M., Katoh, Y., Shiba, T., Yamaguchi, Y., Kato, R., Kato, K., Nakayama, K., Wakatsuki, S.

(2005) FEBS Lett 579: 5385-5391

Released	2005-10-11
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Bos taurus Homo sapiens
Macromolecule	Target of Myb protein 1 (protein) Ubiquitin (protein)

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1WUO \| pdb_00001wuo	Download File View File

Crystal structure of metallo-beta-lactamase IMP-1 mutant (D81A)

Yamaguchi, Y., Yamagata, Y., Goto, M.

(2005) J Biological Chem 280: 20824-20832

Released	2005-03-29
Method	X-RAY DIFFRACTION 2.01 Å
Organisms	Serratia marcescens
Macromolecule	Beta-lactamase IMP-1 (protein)
Unique Ligands	ACY, ZN

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1WUP \| pdb_00001wup	Download File View File

Crystal structure of metallo-beta-lactamase IMP-1 mutant (D81E)

Yamaguchi, Y., Yamagata, Y., Goto, M.

(2005) J Biological Chem 280: 20824-20832

Released	2005-03-29
Method	X-RAY DIFFRACTION 3 Å
Organisms	Serratia marcescens
Macromolecule	Beta-lactamase IMP-1 (protein)
Unique Ligands	ACY, ZN

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1WXS \| pdb_00001wxs	Download File View File

Solution Structure of Ufm1, a ubiquitin-fold modifier

Sasakawa, H., Sakata, E., Yamaguchi, Y., Komatsu, M., Tatsumi, K., Kominami, E., Tanaka, K., Kato, K.

(2006) Biochem Biophys Res Commun 343: 21-26

Released	2006-04-18
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Ubiquitin-fold Modifier 1 (protein)

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1WZ1 \| pdb_00001wz1	Download File View File

Crystal structure of the Fv fragment complexed with dansyl-lysine

Nakasako, M., Oka, T., Mashumo, M., Takahashi, H., Shimada, I., Yamaguchi, Y., Kato, K., Arata, Y.

(2005) J Mol Biology 351: 627-640

Released	2006-01-31
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Mus musculus
Macromolecule	Ig heavy chain (protein) Ig light chain (protein)
Unique Ligands	DNS

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2D5U \| pdb_00002d5u	Download File View File

Solution structure of the N-terminal portion of the PUB domain of mouse peptide:N-glycanase

Sasakawa, H., Hirao, T., Yamaguchi, Y., Suzuki, T., Kato, K.

To be published

Released	2006-11-21
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	N-glycanase 1 (protein)

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2DJJ \| pdb_00002djj	Download File View File

Solution structure of the a' domain of thermophilic fungal protein disulfide isomerase

Kato, K., Yamaguchi, Y.

To be published

Released	2006-04-25
Method	SOLUTION NMR
Organisms	Mycothermus thermophilus
Macromolecule	Protein disulfide-isomerase (protein)

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2DJK \| pdb_00002djk	Download File View File

Solution structure of the b' domain of thermophilic fungal protein disulfide isomerase

Kato, K., Yamaguchi, Y.

To be published

Released	2006-04-25
Method	SOLUTION NMR
Organisms	Mycothermus thermophilus
Macromolecule	Protein disulfide-isomerase (protein)

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2DOO \| pdb_00002doo	Download File View File

The structure of IMP-1 complexed with the detecting reagent (DansylC4SH) by a fluorescent probe

Kurosaki, H., Yamaguchi, Y., Yasuzawa, H., Jin, W., Yamagata, Y., Arakawa, Y.

(2006) ChemMedChem 1: 969-972

Released	2006-11-28
Method	X-RAY DIFFRACTION 2.43 Å
Organisms	Serratia marcescens
Macromolecule	BETA-LACTAMASE IMP-1 (protein)
Unique Ligands	C4H, ZN

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2DPF \| pdb_00002dpf	Download File View File

Crystal Structure of curculin1 homodimer

Kurimoto, E., Suzuki, M., Amemiya, E., Yamaguchi, Y., Nirasawa, S., Shimba, N., Xu, N., Kashiwagi, T., Kawai, M., Suzuki, E., Kato, K.

(2007) J Biological Chem 282: 33252-33256

Released	2007-05-15
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Molineria latifolia
Macromolecule	Curculin (protein)
Unique Ligands	SO4

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2DTS \| pdb_00002dts	Download File View File

Crystal Structure of the Defucosylated Fc Fragment from Human Immunoglobulin G1

Matsumiya, S., Yamaguchi, Y., Saito, J., Nagano, M., Sasakawa, H., Otaki, S., Satoh, M., Shitara, K., Kato, K.

(2007) J Mol Biology 368: 767-779

Released	2007-03-13
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	Ig gamma-1 chain C region (protein)
Unique branched monosaccharides	BMA, MAN, NAG

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2E1Q \| pdb_00002e1q	Download File View File

Crystal Structure of Human Xanthine Oxidoreductase mutant, Glu803Val

Yamaguchi, Y., Matsumura, T., Ichida, K., Okamoto, K., Nishino, T.

(2007) J Biochem 141: 513-524

Released	2007-09-18
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Homo sapiens
Macromolecule	Xanthine dehydrogenase/oxidase (protein)
Unique Ligands	BCT, CA, FAD, FES, MOM, MTE, SAL

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2JZ4 \| pdb_00002jz4	Download File View File

Putative 32 kDa myrosinase binding protein At3g16450.1 from Arabidopsis thaliana

Takeda, N., Sugimori, N., Torizawa, T., Terauchi, T., Ono, A.M., Yagi, H., Yamaguchi, Y., Kato, K., Ikeya, T., Guntert, P., Aceti, D.J., Markley, J.L., Kainosho, M., Center for Eukaryotic Structural Genomics (CESG)

(2008) FEBS J 275: 5873-5884

Released	2008-02-19
Method	SOLUTION NMR
Organisms	Arabidopsis thaliana
Macromolecule	Jasmonate inducible protein isolog (protein)

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2KP1 \| pdb_00002kp1	Download File View File

Solution structure of the a' domain of thermophilic fungal protein disulfide isomerase

Kato, K., Yamaguchi, Y., Serve, O.

(2009) J Mol Biology

Released	2009-10-27
Method	SOLUTION NMR
Organisms	Mycothermus thermophilus
Macromolecule	Protein disulfide-isomerase (protein)

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2KP2 \| pdb_00002kp2	Download File View File

Solution structure of the b' domain of thermophilic fungal protein disulfide isomerase

Kato, K., Yamaguchi, Y., Serve, O.

(2009) J Mol Biology

Released	2009-10-27
Method	SOLUTION NMR
Organisms	Mycothermus thermophilus
Macromolecule	Protein disulfide-isomerase (protein)

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2RQY \| pdb_00002rqy	Download File View File

Solution structure and dynamics of mouse ARMET

Hoseki, J., Sasakawa, H., Yamaguchi, Y., Maeda, M., Kubota, H., Kato, K., Nagata, K.

(2010) FEBS Lett 584: 1536-1542

Released	2010-04-21
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	Putative uncharacterized protein (protein)

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2YZ3 \| pdb_00002yz3	Download File View File

Crystallographic Investigation of Inhibition Mode of the VIM-2 Metallo-beta-lactamase from Pseudomonas aeruginosa with Mercaptocarboxylate Inhibitor

Yamaguchi, Y., Yamagata, Y., Arakawa, Y., Kurosaki, H.

(2007) J Med Chem 50: 6647-6653

Released	2008-03-11
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Pseudomonas putida
Macromolecule	Metallo-beta-lactamase (protein)
Unique Ligands	M5P, SO4, ZN

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2ZCB \| pdb_00002zcb	Download File View File

Crystal Structure of ubiquitin P37A/P38A

Kitahara, R., Tanaka, T., Sakata, E., Yamaguchi, Y., Kato, K., Yokoyama, S.

To be published

Released	2007-11-20
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Homo sapiens
Macromolecule	Ubiquitin (protein)
Unique Ligands	ZN

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2ZJ9 \| pdb_00002zj9	Download File View File

X-ray crystal structure of AmpC beta-Lactamase (AmpC(D)) from an Escherichia coli with a Tripeptide Deletion (Gly286 Ser287 Asp288) on the H10 Helix

Yamaguchi, Y., Sato, G., Yamagata, Y., Wachino, J., Arakawa, Y., Kurosaki, H.

(2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 540-543

Released	2009-03-10
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Escherichia coli
Macromolecule	AmpC (protein)
Unique Ligands	IPA, NA

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3A33 \| pdb_00003a33	Download File View File

UbcH5b~Ubiquitin Conjugate

Sakata, E., Satoh, T., Yamamoto, S., Yamaguchi, Y., Yagi-Utsumi, M., Kurimoto, E., Wakatsuki, S., Kato, K.

(2010) Structure 18: 138-147

Released	2009-11-24
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Homo sapiens
Macromolecule	Ubiquitin (protein) Ubiquitin-conjugating enzyme E2 D2 (protein)
Unique Ligands	GOL

1 to 25 of 80 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

1IYF | pdb_00001iyf

1UMH | pdb_00001umh

1UMI | pdb_00001umi

1VGN | pdb_00001vgn

1WR6 | pdb_00001wr6

1WRD | pdb_00001wrd

1WUO | pdb_00001wuo

1WUP | pdb_00001wup

1WXS | pdb_00001wxs

1WZ1 | pdb_00001wz1

2D5U | pdb_00002d5u

2DJJ | pdb_00002djj

2DJK | pdb_00002djk

2DOO | pdb_00002doo

2DPF | pdb_00002dpf

2DTS | pdb_00002dts

2E1Q | pdb_00002e1q

2JZ4 | pdb_00002jz4

2KP1 | pdb_00002kp1

2KP2 | pdb_00002kp2

2RQY | pdb_00002rqy

2YZ3 | pdb_00002yz3

2ZCB | pdb_00002zcb

2ZJ9 | pdb_00002zj9

3A33 | pdb_00003a33