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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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Search Summary

This query matches 30 Structures.

Refinements

Structure Determination Methodology

experimental (30)

Scientific Name of Source Organism

	Tequatrovirus T4 (7)
	Nitratidesulfovibrio vulgaris str. 'Miyazaki F (6)
	Clitoria ternatea (5)
	Methanocaldococcus jannaschii (3)
	Pyrococcus furiosus DSM 3638 (3)
	Saccharomyces cerevisiae S288C (3)
	Comamonas testosteroni (2)
	Homo sapiens (2)
	Bos taurus (1)

Taxonomy

	Eukaryota (11)
	Bacteria (8)
	Duplodnaviria (7)
	Archaea (6)

Experimental Method

	X-RAY DIFFRACTION (30)
	NEUTRON DIFFRACTION (2)

Polymer Entity Type

Protein (30)

Refinement Resolution (Å)

	1.0 - 1.5 (6)
	1.5 - 2.0 (15)
	2.0 - 2.5 (5)
	2.5 - 3.0 (5)
	4.0 - 4.5 (1)

Release Date

	2005 - 2009 (5)
	2010 - 2014 (7)
	2015 - 2019 (11)
	2020 - 2024 (7)

Enzyme Classification Name

	Oxidoreductases (12)
	Transferases (6)
	Hydrolases (7)
	Translocases (1)
	Ligases (1)

Membrane Protein Annotation

	PDBTM (1)
	mpstruc (1)

Symmetry Type

	Asymmetric (22)
	Cyclic (9)

SCOP Classification

	Membrane and cell surface proteins and peptides (1)
	Alpha and beta proteins (a/b) (9)
	Multi-domain proteins (alpha and beta) (5)
	Artifacts (1)
	All alpha proteins (4)
	Alpha and beta proteins (a+b) (3)
	All beta proteins (1)
	Small proteins (1)

AllSelected

1 to 25 of 30 Structures

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2DKH \| pdb_00002dkh	Download File View File

Crystal structure of 3-hydroxybenzoate hydroxylase from Comamonas testosteroni, in complex with the substrate

Hiromoto, T., Fujiwara, S., Hosokawa, K., Yamaguchi, H.

(2006) J Mol Biology 364: 878-896

Released	2006-10-24
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Comamonas testosteroni
Macromolecule	3-hydroxybenzoate hydroxylase (protein)
Unique Ligands	3HB, FAD, SO4

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2DKI \| pdb_00002dki	Download File View File

Crystal structure of 3-hydroxybenzoate hydroxylase from Comamonas testosteroni, under pressure of xenon gas (12 atm)

Hiromoto, T., Fujiwara, S., Hosokawa, K., Yamaguchi, H.

(2006) J Mol Biology 364: 878-896

Released	2006-10-24
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Comamonas testosteroni
Macromolecule	3-HYDROXYBENZOATE HYDROXYLASE (protein)
Unique Ligands	FAD, SO4, XE

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3AUL \| pdb_00003aul	Download File View File

Crystal structure of wild-type Lys48-linked diubiquitin in an open conformation

Hirano, T., Olivier, S., Yagi, M., Takemoto, E., Hiromoto, T., Satoh, T., Mizushima, T., Kato, K.

(2011) J Biological Chem 286: 37496-37502

Released	2011-09-07
Method	X-RAY DIFFRACTION 2.39 Å
Organisms	Homo sapiens
Macromolecule	Polyubiquitin-C (protein)

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3F46 \| pdb_00003f46	Download File View File

The Crystal Structure of C176A Mutated [Fe]-Hydrogenase (Hmd) Holoenzyme from Methanocaldococcus jannaschii

Hiromoto, T., Vogt, S., Warkentin, E., Thauer, R.K., Shima, S., Ermler, U.

(2009) FEBS Lett 583: 585-590

Released	2009-02-10
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Methanocaldococcus jannaschii
Macromolecule	5,10-methenyltetrahydromethanopterin hydrogenase (protein)
Unique Ligands	CMO, DTV, FE2, I2C

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3F47 \| pdb_00003f47	Download File View File

The Crystal Structure of [Fe]-Hydrogenase (Hmd) Holoenzyme from Methanocaldococcus jannaschii

Hiromoto, T., Pilak, O., Warkentin, E., Thauer, R.K., Shima, S., Ermler, U.

(2009) FEBS Lett 583: 585-590

Released	2009-02-10
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Methanocaldococcus jannaschii
Macromolecule	5,10-methenyltetrahydromethanopterin hydrogenase (protein)
Unique Ligands	CMO, FE2, I2C, NA

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3H65 \| pdb_00003h65	Download File View File

The Crystal Structure of C176A Mutated [Fe]-Hydrogenase (Hmd) Holoenzyme in Complex with Methylenetetrahydromethanopterin

Hiromoto, T., Warkentin, E., Shima, S., Ermler, U.

(2009) Angew Chem Int Ed Engl 48: 6457-6460

Released	2009-09-01
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Methanocaldococcus jannaschii
Macromolecule	5,10-methenyltetrahydromethanopterin hydrogenase (protein)
Unique Ligands	CMO, DTV, FE2, H4M, I2C

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3VR0 \| pdb_00003vr0	Download File View File

Crystal structure of Pyrococcus furiosus PbaB, an archaeal proteasome activator

Kumoi, K., Satoh, T., Hiromoto, T., Mizushima, T., Kamiya, Y., Noda, M., Uchiyama, S., Murata, K., Yagi, H., Kato, K.

(2013) PLoS One 8: e60294-e60294

Released	2013-04-03
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Pyrococcus furiosus DSM 3638
Macromolecule	Putative uncharacterized protein (protein)
Unique Ligands	AU

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3WC4 \| pdb_00003wc4	Download File View File

Crystal structure of UDP-glucose: anthocyanidin 3-O-glucosyltransferase from Clitoria ternatea

Hiromoto, T., Honjo, E., Tamada, T., Kuroki, R.

(2013) J Synchrotron Radiat 20: 894-898

Released	2013-10-30
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Clitoria ternatea
Macromolecule	UDP-glucose:anthocyanidin 3-O-glucosyltransferase (protein)
Unique Ligands	ACT, GOL

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3WHJ \| pdb_00003whj	Download File View File

Crystal structure of Nas2 N-terminal domain

Satoh, T., Saeki, Y., Hiromoto, T., Wang, Y.-H., Uekusa, Y., Yagi, H., Yoshihara, H., Yagi-Utsumi, M., Mizushima, T., Tanaka, K., Kato, K.

(2014) Structure 22: 731-743

Released	2014-03-26
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Probable 26S proteasome regulatory subunit p27 (protein)
Unique Ligands	CD, SO4

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3WHK \| pdb_00003whk	Download File View File

Crystal structure of PAN-Rpt5C chimera

Satoh, T., Saeki, Y., Hiromoto, T., Wang, Y.-H., Uekusa, Y., Yagi, H., Yoshihara, H., Yagi-Utsumi, M., Mizushima, T., Tanaka, K., Kato, K.

(2014) Structure 22: 731-743

Released	2014-03-26
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Pyrococcus furiosus DSM 3638 Saccharomyces cerevisiae S288C
Macromolecule	Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A (protein)
Unique Ligands	ATP

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3WHL \| pdb_00003whl	Download File View File

Crystal structure of Nas2 N-terminal domain complexed with PAN-Rpt5C chimera

Satoh, T., Saeki, Y., Hiromoto, T., Wang, Y.-H., Uekusa, Y., Yagi, H., Yoshihara, H., Yagi-Utsumi, M., Mizushima, T., Tanaka, K., Kato, K.

(2014) Structure 22: 731-743

Released	2014-03-26
Method	X-RAY DIFFRACTION 4 Å
Organisms	Pyrococcus furiosus DSM 3638 Saccharomyces cerevisiae S288C
Macromolecule	Probable 26S proteasome regulatory subunit p27 (protein) Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A (protein)
Unique Ligands	ATP

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4DBG \| pdb_00004dbg	Download File View File

Crystal structure of HOIL-1L-UBL complexed with a HOIP-UBA derivative

Yagi, H., Hiromoto, T., Mizushima, T., Kurimoto, E., Kato, K.

(2012) EMBO Rep 13: 462-468

Released	2012-04-04
Method	X-RAY DIFFRACTION 2.71 Å
Organisms	Homo sapiens
Macromolecule	RING finger protein 31 (protein) RanBP-type and C3HC4-type zinc finger-containing protein 1 (protein)

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4REL \| pdb_00004rel	Download File View File

Crystal structure of UDP-glucose: anthocyanidin 3-O-glucosyltransferase in complex with kaempferol

Hiromoto, T., Honjo, E., Tamada, T., Kuroki, R.

(2015) Protein Sci 24: 395-407

Released	2015-01-21
Method	X-RAY DIFFRACTION 1.754 Å
Organisms	Clitoria ternatea
Macromolecule	UDP-glucose:anthocyanidin 3-O-glucosyltransferase (protein)
Unique Ligands	ACT, GOL, KMP

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4REM \| pdb_00004rem	Download File View File

Crystal structure of UDP-glucose: anthocyanidin 3-O-glucosyltransferase in complex with delphinidin

Hiromoto, T., Honjo, E., Tamada, T., Kuroki, R.

(2015) Protein Sci 24: 395-407

Released	2015-01-21
Method	X-RAY DIFFRACTION 2.55 Å
Organisms	Clitoria ternatea
Macromolecule	UDP-glucose:anthocyanidin 3-O-glucosyltransferase (protein)
Unique Ligands	DLM, GOL

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4REN \| pdb_00004ren	Download File View File

Crystal structure of UDP-glucose: anthocyanidin 3-O-glucosyltransferase in complex with petunidin

Hiromoto, T., Honjo, E., Tamada, T., Kuroki, R.

(2015) Protein Sci 24: 395-407

Released	2015-01-21
Method	X-RAY DIFFRACTION 2.704 Å
Organisms	Clitoria ternatea
Macromolecule	UDP-glucose:anthocyanidin 3-O-glucosyltransferase (protein)
Unique Ligands	GOL, P5M

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4WHM \| pdb_00004whm	Download File View File

Crystal structure of UDP-glucose: anthocyanidin 3-O-glucosyltransferase in complex with UDP

Hiromoto, T., Honjo, E., Tamada, T., Kuroki, R.

(2015) Protein Sci 24: 395-407

Released	2015-01-21
Method	X-RAY DIFFRACTION 1.851 Å
Organisms	Clitoria ternatea
Macromolecule	UDP-glucose:anthocyanidin 3-O-glucosyltransferase (protein)
Unique Ligands	ACT, GOL, UDP

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5XLE \| pdb_00005xle	Download File View File

Crystal structure of anaerobically purified and anaerobically crystallized D. vulgaris Miyazaki F [NiFe]-hydrogenase

Nishikawa, K., Mochida, S., Hiromoto, T., Shibata, N., Higuchi, Y.

(2017) J Inorg Biochem 177: 435-437

Released	2018-06-06
Method	X-RAY DIFFRACTION 1.69 Å
Organisms	Nitratidesulfovibrio vulgaris str. 'Miyazaki F
Macromolecule	Periplasmic [NiFe] hydrogenase large subunit (protein) Periplasmic [NiFe] hydrogenase small subunit (protein)
Unique Ligands	F3S, MG, MPD, NFU, SF4, TRS

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5XLF \| pdb_00005xlf	Download File View File

Crystal structure of aerobically purified and aerobically crystallized D. vulgaris Miyazaki F [NiFe]-hydrogenase

Nishikawa, K., Mochida, S., Hiromoto, T., Shibata, N., Higuchi, Y.

(2017) J Inorg Biochem 177: 435-437

Released	2018-06-06
Method	X-RAY DIFFRACTION 1.71 Å
Organisms	Nitratidesulfovibrio vulgaris str. 'Miyazaki F
Macromolecule	Periplasmic [NiFe] hydrogenase large subunit (protein) Periplasmic [NiFe] hydrogenase small subunit (protein)
Unique Ligands	F3S, MG, MPD, NFV, SF4

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5XLG \| pdb_00005xlg	Download File View File

Crystal structure of anaerobically purified and aerobically crystallized D. vulgaris Miyazaki F [NiFe]-hydrogenase

Nishikawa, K., Mochida, S., Hiromoto, T., Shibata, N., Higuchi, Y.

(2017) J Inorg Biochem 177: 435-437

Released	2018-06-06
Method	X-RAY DIFFRACTION 1.64 Å
Organisms	Nitratidesulfovibrio vulgaris str. 'Miyazaki F
Macromolecule	Periplasmic [NiFe] hydrogenase large subunit (protein) Periplasmic [NiFe] hydrogenase small subunit (protein)
Unique Ligands	F3S, MG, MPD, NFV, SF4, TRS

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5XLH \| pdb_00005xlh	Download File View File

Crystal structure of aerobically purified and aerobically crystallized for 12weeks D. vulgaris Miyazaki F [NiFe]-hydrogenase

Nishikawa, K., Mochida, S., Hiromoto, T., Shibata, N., Higuchi, Y.

(2017) J Inorg Biochem 177: 435-437

Released	2018-06-06
Method	X-RAY DIFFRACTION 1.93 Å
Organisms	Nitratidesulfovibrio vulgaris str. 'Miyazaki F
Macromolecule	Periplasmic [NiFe] hydrogenase large subunit (protein) Periplasmic [NiFe] hydrogenase small subunit (protein)
Unique Ligands	F3S, MG, MPD, NFV, SF4

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5XPE \| pdb_00005xpe	Download File View File

Neutron structure of the T26H mutant of T4 lysozyme

Hiromoto, T., Kuroki, R.

(2017) Protein Sci 26: 1953-1963

Released	2017-10-04
Method	X-RAY DIFFRACTION 1.648 Å NEUTRON DIFFRACTION 2.09 Å
Organisms	Tequatrovirus T4
Macromolecule	Endolysin (protein)
Unique Ligands	CL, NA

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5XPF \| pdb_00005xpf	Download File View File

High-resolution X-ray structure of the T26H mutant of T4 lysozyme

Hiromoto, T., Kuroki, R.

(2017) Protein Sci 26: 1953-1963

Released	2017-10-04
Method	X-RAY DIFFRACTION 1.04 Å
Organisms	Tequatrovirus T4
Macromolecule	Endolysin (protein)
Unique Ligands	CL, GOL, HEZ, NA

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5Y4N \| pdb_00005y4n	Download File View File

Crystal structure of aerobically purified and anaerobically crystallized D. vulgaris Miyazaki F [NiFe]-hydrogenase

Nishikawa, K., Mochida, S., Hiromoto, T., Shibata, N., Higuchi, Y.

(2017) J Inorg Biochem 177: 435-437

Released	2018-08-08
Method	X-RAY DIFFRACTION 1.69 Å
Organisms	Nitratidesulfovibrio vulgaris str. 'Miyazaki F
Macromolecule	Periplasmic [NiFe] hydrogenase large subunit (protein) Periplasmic [NiFe] hydrogenase small subunit (protein)
Unique Ligands	F3S, MG, MPD, MRD, NFU, SF4, TRS

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6JUW \| pdb_00006juw	Download File View File

BOVINE HEART CYTOCHROME C OXIDASE IN CATALITIC INTERMEDIATES AT 1.80 ANGSTROM RESOLUTION

Shimada, A., Muramoto, K., Shinzawa-Itoh, K., Yoshikawa, S., Tsukihara, T.

(2020) J Biological Chem 295: 5818-5833

Released	2020-03-25
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Bos taurus
Macromolecule	Unique protein chains: 13
Unique Ligands	CDL, CHD, CU, CUA, DMU, EDO, HEA, MG, NA, PEK, PGV, PO4, PSC, TGL, ZN