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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Hirata, K."

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Search Summary

This query matches 146 Structures.

Refinements

Structure Determination Methodology

experimental (146)

Scientific Name of Source Organism

	Homo sapiens (44)
	Bombyx mori cypovirus 1 (24)
	Bos taurus (11)
	Fusarium oxysporum (9)
	Geobacillus thermodenitrificans NG80-2 (9)
	Tequatrovirus T4 (8)
	Bradyrhizobium sp. ORS 375 (7)
	Equus caballus (7)
	Escherichia coli (7)
	Chlamydomonas reinhardtii (6)

More...

Taxonomy

	Eukaryota (97)
	Bacteria (34)
	Riboviria (24)
	Duplodnaviria (13)
	Archaea (3)
	other sequences (3)

Experimental Method

X-RAY DIFFRACTION (146)

Polymer Entity Type

Protein (146)

Refinement Resolution (Å)

	1.0 - 1.5 (26)
	1.5 - 2.0 (54)
	2.0 - 2.5 (28)
	2.5 - 3.0 (21)
	3.0 - 3.5 (12)
	3.5 - 4.0 (5)

Release Date

	2005 - 2009 (13)
	2010 - 2014 (8)
	2015 - 2019 (78)
	2020 - 2024 (47)

Enzyme Classification Name

	Oxidoreductases (49)
	Hydrolases (29)
	Translocases (11)
	Transferases (1)

Membrane Protein Annotation

	PDBTM (48)
	MemProtMD (35)
	mpstruc (28)
	OPM (18)

Symmetry Type

	Asymmetric (77)
	Cyclic (50)
	Tetrahedral (16)
	Octahedral (5)

SCOP Classification

	Membrane and cell surface proteins and peptides (12)
	All beta proteins (43)
	All alpha proteins (29)
	Small proteins (10)
	Alpha and beta proteins (a+b) (9)
	Artifacts (11)
	Alpha and beta proteins (a/b) (2)

AllSelected

1 to 25 of 146 Structures

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1WUA \| pdb_00001wua	Download File View File

The structure of Aplyronine A-actin complex

Hirata, K., Muraoka, S., Suenaga, K., Kuroda, T., Kato, K., Tanaka, H., Yamamoto, M., Takata, M., Yamada, K., Kigoshi, H.

(2006) J Mol Biology 356: 945-954

Released	2006-02-14
Method	X-RAY DIFFRACTION 1.45 Å
Organisms	Oryctolagus cuniculus
Macromolecule	Actin, alpha skeletal muscle (protein)
Unique Ligands	AP8, ATP, CA

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2EIJ \| pdb_00002eij	Download File View File

Bovine heart cytochrome C oxidase in the fully reduced state

Muramoto, K., Hirata, K., Shinzawa-Itoh, K., Yoko-o, S., Yamashita, E., Aoyama, H., Tsukihara, T., Yoshikawa, S.

(2007) Proc Natl Acad Sci U S A 104: 7881-7886

Released	2007-05-29
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Bos taurus
Macromolecule	Unique protein chains: 13
Unique Ligands	CDL, CHD, CU, CUA, DMU, HEA, MG, NA, PEK, PGV, PSC, TGL, ZN

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2EIK \| pdb_00002eik	Download File View File

Cadmium ion binding structure of bovine heart cytochrome C oxidase in the fully reduced state

Muramoto, K., Hirata, K., Shinzawa-Itoh, K., Yoko-O, S., Yamashita, E., Aoyama, H., Tsukihara, T., Yoshikawa, S.

(2007) Proc Natl Acad Sci U S A 104: 7881-7886

Released	2007-05-29
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Bos taurus
Macromolecule	Unique protein chains: 13
Unique Ligands	CD, CDL, CHD, CU, CUA, DMU, HEA, MG, NA, PEK, PGV, PSC, TGL, ZN

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2EIL \| pdb_00002eil	Download File View File

Cadmium ion binding structure of bovine heart cytochrome C oxidase in the fully oxidized state

Muramoto, K., Hirata, K., Shinzawa-Itoh, K., Yoko-o, S., Yamashita, E., Aoyama, H., Tsukihara, T., Yoshikawa, S.

(2007) Proc Natl Acad Sci U S A 104: 7881-7886

Released	2007-05-29
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Bos taurus
Macromolecule	Unique protein chains: 13
Unique Ligands	CD, CDL, CHD, CU, CUA, DMU, HEA, MG, NA, PEK, PGV, PSC, TGL, ZN

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2EIM \| pdb_00002eim	Download File View File

Zinc ion binding structure of bovine heart cytochrome C oxidase in the fully reduced state

Muramoto, K., Hirata, K., Shinzawa-Itoh, K., Yoko-o, S., Yamashita, E., Aoyama, H., Tsukihara, T., Yoshikawa, S.

(2007) Proc Natl Acad Sci U S A 104: 7881-7886

Released	2007-05-29
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Bos taurus
Macromolecule	Unique protein chains: 13
Unique Ligands	CDL, CHD, CU, CUA, DMU, HEA, MG, NA, PEK, PGV, PSC, TGL, ZN

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2EIN \| pdb_00002ein	Download File View File

Zinc ion binding structure of bovine heart cytochrome C oxidase in the fully oxidized state

Muramoto, K., Hirata, K., Shinzawa-Itoh, K., Yoko-o, S., Yamashita, E., Aoyama, H., Tsukihara, T., Yoshikawa, S.

(2007) Proc Natl Acad Sci U S A 104: 7881-7886

Released	2007-05-29
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Bos taurus
Macromolecule	Unique protein chains: 13
Unique Ligands	CDL, CHD, CU, CUA, DMU, HEA, MG, NA, PEK, PGV, PSC, TGL, ZN

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2PJZ \| pdb_00002pjz	Download File View File

The crystal structure of putative Cobalt transport ATP-binding protein (cbiO-2), ST1066

Hirata, K., Hasegawa, K., Ebihara, A., Yamamoto, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2008-04-22
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Sulfurisphaera tokodaii
Macromolecule	Hypothetical protein ST1066 (protein)
Unique Ligands	SO4

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2Z5P \| pdb_00002z5p	Download File View File

Apo-Fr with low content of Pd ions

Ueno, T., Hirata, K., Abe, M., Suzuki, M., Abe, S., Shimizu, N., Yamamoto, M., Takata, M., Watanabe, Y.

(2009) J Am Chem Soc 131: 5094-5100

Released	2008-07-29
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Equus caballus
Macromolecule	Ferritin light chain (protein)
Unique Ligands	CD, GOL, PD, SO4

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2Z5Q \| pdb_00002z5q	Download File View File

Apo-Fr with intermediate content of Pd ion

Ueno, T., Hirata, K., Abe, M., Suzuki, M., Abe, S., Shimizu, N., Yamamoto, M., Takata, M., Watanabe, Y.

(2009) J Am Chem Soc 131: 5094-5100

Released	2008-07-29
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Equus caballus
Macromolecule	Ferritin light chain (protein)
Unique Ligands	CD, GOL, PD

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2Z5R \| pdb_00002z5r	Download File View File

Apo-Fr with high content of Pd ions

Ueno, T., Hirata, K., Abe, M., Suzuki, M., Abe, S., Shimizu, N., Yamamoto, M., Takata, M., Watanabe, Y.

(2009) J Am Chem Soc 131: 5094-5100

Released	2008-07-29
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Equus caballus
Macromolecule	Ferritin light chain (protein)
Unique Ligands	CD, PD

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2ZUR \| pdb_00002zur	Download File View File

Crystal Structure of Rh(nbd)/apo-Fr

Abe, S., Hirata, K., Ueno, T., Shimizu, N., Yamamoto, M., Takata, M., Watanabe, Y.

(2009) J Am Chem Soc 131: 6958-6960

Released	2009-06-02
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Equus caballus
Macromolecule	Ferritin light chain (protein)
Unique Ligands	CD, EDO, RH, SO4

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2ZXW \| pdb_00002zxw	Download File View File

Bovine heart cytochrome c oxidase at the fully oxidized state (1-s X-ray exposure dataset)

Aoyama, H., Muramoto, K., Shinzawa-Itoh, K., Hirata, K., Yamashita, E., Tsukihara, T., Ogura, T., Yoshikawa, S.

(2009) Proc Natl Acad Sci U S A 106: 2165-2169

Released	2009-02-24
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Bos taurus
Macromolecule	Unique protein chains: 13
Unique Ligands	CDL, CHD, CU, CUA, DMU, HEA, MG, NA, PEK, PER, PGV, PSC, TGL, UNX, ZN

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3FI6 \| pdb_00003fi6	Download File View File

apo-H49AFr with high content of Pd ions

Abe, M., Ueno, T., Hirata, K., Suzuki, M., Abe, S., Shimizu, N., Yamaoto, M., Takata, M., Watanabe, Y.

(2009) J Am Chem Soc 131: 5094-5100

Released	2009-04-07
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Equus caballus
Macromolecule	Ferritin light chain (protein)
Unique Ligands	CD, PD, SO4

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3WFT \| pdb_00003wft	Download File View File

Crystal structure of horse heart myoglobin reconstituted with cobalt(II) tetradehydrocorrin

Mizohata, E., Morita, Y., Oohora, K., Hirata, K., Ohbayashi, J., Inoue, T., Hisaeda, Y., Hayashi, T.

(2014) Chem Commun (Camb) 50: 12560-12563

Released	2014-12-03
Method	X-RAY DIFFRACTION 1.3 Å
Organisms	Equus caballus
Macromolecule	Myoglobin (protein)
Unique Ligands	GOL, J1R, J1S, SO4

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3WFU \| pdb_00003wfu	Download File View File

Crystal structure of horse heart myoglobin reconstituted with cobalt(I) tetradehydrocorrin

Mizohata, E., Morita, Y., Oohora, K., Hirata, K., Ohbayashi, J., Inoue, T., Hisaeda, Y., Hayashi, T.

(2014) Chem Commun (Camb) 50: 12560-12563

Released	2014-12-03
Method	X-RAY DIFFRACTION 1.35 Å
Organisms	Equus caballus
Macromolecule	Myoglobin (protein)
Unique Ligands	J1R, J1S, SO4

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3WG7 \| pdb_00003wg7	Download File View File

A 1.9 angstrom radiation damage free X-ray structure of large (420KDa) protein by femtosecond crystallography

Hirata, K., Shinzawa-Itoh, K., Yano, N., Takemura, S., Kato, K., Hatanaka, M., Muramoto, K., Kawahara, T., Tsukihara, T., Yamashita, E., Tono, K., Ueno, G., Hikima, T., Murakami, H., Inubushi, Y., Yabashi, M., Ishikawa, T., Yamamoto, M., Ogura, T., Sugimoto, H., Shen, J.R., Yoshikawa, S., Ago, H.

(2014) Nat Methods 11: 734-736

Released	2014-04-30
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Bos taurus
Macromolecule	Unique protein chains: 13
Unique Ligands	CDL, CHD, CU, CUA, DMU, HEA, MG, NA, PEK, PER, PGV, PSC, TGL, ZN

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4CBQ \| pdb_00004cbq	Download File View File

Crystal structure of the thioredoxin reductase from Entamoeba histolytica with auranofin Au(I) bound to Cys286

Parsonage, D., Kells, P.M., Hirata, K., Debnath, A., Poole, L.B., McKerrow, J.H., Reed, S.L., Podust, L.M.

(2016) J Struct Biol 194: 180

Released	2014-11-05
Method	X-RAY DIFFRACTION 1.94 Å
Organisms	Entamoeba histolytica
Macromolecule	THIOREDOXIN REDUCTASE (protein)
Unique Ligands	AU, CL, FAD, NDP, SO4

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4CCQ \| pdb_00004ccq	Download File View File

Crystal structure of the thioredoxin reductase from Entamoeba histolytica with NADP

Parsonage, D., Kells, P.M., Hirata, K., Debnath, A., Poole, L.B., McKerrow, J.H., Reed, S.L., Podust, L.M.

(2016) J Struct Biol 194: 180

Released	2014-11-05
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Entamoeba histolytica
Macromolecule	THIOREDOXIN REDUCTASE (protein)
Unique Ligands	ACT, EDO, FAD, NAP

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4CCR \| pdb_00004ccr	Download File View File

Crystal structure of the thioredoxin reductase apoenzyme from Entamoeba histolytica in the absence of the NADP cofactor

Parsonage, D., Kells, P.M., Hirata, K., Debnath, A., Poole, L.B., McKerrow, J.H., Reed, S.L., Podust, L.M.

(2016) J Struct Biol 194: 180

Released	2014-11-05
Method	X-RAY DIFFRACTION 2.28 Å
Organisms	Entamoeba histolytica
Macromolecule	THIOREDOXIN REDUCTASE (protein)
Unique Ligands	AU, FAD

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4CW9 \| pdb_00004cw9	Download File View File

Entamoeba histolytica thiredoxin C34S mutant

Parsonage, D., Kells, P.M., Vieira, D.F., Hirata, K., Debnath, A., Poole, L.B., McKerrow, J.H., Reed, S.L., Podust, L.M.

(2016) J Struct Biol 194: 180

Released	2015-05-13
Method	X-RAY DIFFRACTION 1.84 Å
Organisms	Entamoeba histolytica HM-3:IMSS
Macromolecule	THIOREDOXIN (protein)

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4UB6 \| pdb_00004ub6	Download File View File

Native structure of photosystem II (dataset-1) by a femtosecond X-ray laser

Suga, M., Akita, F., Hirata, K., Ueno, G., Murakami, H., Nakajima, Y., Shimizu, T., Yamashita, K., Yamamoto, M., Ago, H., Shen, J.R.

(2015) Nature 517: 99-103

Released	2014-12-03
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Thermostichus vulcanus
Macromolecule	Unique protein chains: 20
Unique Ligands	BCR, BCT, CA, CL, CLA, DGD, FE2, GOL, HEC, HEM, HTG, LHG, LMG, LMT, MG, OEX, PHO, PL9, SQD, UNL

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4UB8 \| pdb_00004ub8	Download File View File

Native structure of photosystem II (dataset-2) by a femtosecond X-ray laser

Suga, M., Akita, F., Hirata, K., Ueno, G., Murakami, H., Nakajima, Y., Shimizu, T., Yamashita, K., Yamamoto, M., Ago, H., Shen, J.R.

(2015) Nature 517: 99-103

Released	2014-12-03
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Thermostichus vulcanus
Macromolecule	Unique protein chains: 20
Unique Ligands	BCR, BCT, CA, CL, CLA, DGD, FE2, GOL, HEC, HEM, HTG, LHG, LMG, LMT, MG, OEX, PHO, PL9, SQD, UNL

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4YSA \| pdb_00004ysa	Download File View File

Completely oxidized structure of copper nitrite reductase from Geobacillus thermodenitrificans

Fukuda, Y., Tse, K.M., Suzuki, M., Diederichs, K., Hirata, K., Nakane, T., Sugahara, M., Nango, E., Tono, K., Joti, Y., Kameshima, T., Song, C., Hatsui, T., Yabashi, M., Nureki, O., Matsumura, H., Inoue, T., Iwata, S., Mizohata, E.

(2016) J Biochem 159: 527-538

Released	2016-02-24
Method	X-RAY DIFFRACTION 1.43 Å
Organisms	Geobacillus thermodenitrificans NG80-2
Macromolecule	Nitrite reductase (protein)
Unique Ligands	CU, NA

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4YSC \| pdb_00004ysc	Download File View File

Completely oxidized structure of copper nitrite reductase from Alcaligenes faecalis

(2016) Proc Natl Acad Sci U S A 113: 2928-2933

Released	2016-03-09
Method	X-RAY DIFFRACTION 2.03 Å
Organisms	Alcaligenes faecalis
Macromolecule	Copper-containing nitrite reductase (protein)
Unique Ligands	CL, CU

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4YSD \| pdb_00004ysd	Download File View File

Room temperature structure of copper nitrite reductase from Geobacillus thermodenitrificans

(2016) J Biochem 159: 527-538

Released	2016-02-24
Method	X-RAY DIFFRACTION 1.35 Å
Organisms	Geobacillus thermodenitrificans NG80-2
Macromolecule	Nitrite reductase (protein)
Unique Ligands	ACY, CU

1 to 25 of 146 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

1WUA | pdb_00001wua

2EIJ | pdb_00002eij

2EIK | pdb_00002eik

2EIL | pdb_00002eil

2EIM | pdb_00002eim

2EIN | pdb_00002ein

2PJZ | pdb_00002pjz

2Z5P | pdb_00002z5p

2Z5Q | pdb_00002z5q

2Z5R | pdb_00002z5r

2ZUR | pdb_00002zur

2ZXW | pdb_00002zxw

3FI6 | pdb_00003fi6

3WFT | pdb_00003wft

3WFU | pdb_00003wfu

3WG7 | pdb_00003wg7

4CBQ | pdb_00004cbq

4CCQ | pdb_00004ccq

4CCR | pdb_00004ccr

4CW9 | pdb_00004cw9

4UB6 | pdb_00004ub6

4UB8 | pdb_00004ub8

4YSA | pdb_00004ysa

4YSC | pdb_00004ysc

4YSD | pdb_00004ysd