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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Sakamoto, T."

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Search Summary

This query matches 40 Structures.

Refinements

Structure Determination Methodology

experimental (40)

Scientific Name of Source Organism

	Fusarium oxysporum (8)
	Penicillium chrysogenum (6)
	Homo sapiens (5)
	Eisenia fetida (4)
	Solanum lycopersicum (4)
	Thermostichus vulcanus (4)
	Pyrococcus furiosus DSM 3638 (2)
	Escherichia coli (1)
	Hepatitis B virus (1)
	Penaeus japonicus (1)

Taxonomy

	Eukaryota (28)
	Bacteria (5)
	Archaea (2)
	Riboviria (1)

Experimental Method

	X-RAY DIFFRACTION (30)
	SOLUTION NMR (10)
	NEUTRON DIFFRACTION (1)

Polymer Entity Type

	Protein (34)
	RNA (8)

Refinement Resolution (Å)

	1.0 - 1.5 (8)
	1.5 - 2.0 (8)
	2.0 - 2.5 (5)
	2.5 - 3.0 (8)
	3.0 - 3.5 (2)

Release Date

	2000 - 2004 (1)
	2005 - 2009 (5)
	2010 - 2014 (4)
	2015 - 2019 (16)
	2020 - 2024 (14)

Enzyme Classification Name

	Hydrolases (13)
	Oxidoreductases (4)
	Lyases (5)
	Transferases (1)

Membrane Protein Annotation

	MemProtMD (4)
	PDBTM (4)
	mpstruc (4)

Symmetry Type

	Asymmetric (27)
	Cyclic (7)

SCOP Classification

	Membrane and cell surface proteins and peptides (4)
	All alpha proteins (4)
	Artifacts (5)
	All beta proteins (1)
	Alpha and beta proteins (a+b) (2)
	Alpha and beta proteins (a/b) (1)

AllSelected

1 to 25 of 40 Structures

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1L1W \| pdb_00001l1w	Download File View File

NMR structure of a SRP19 binding domain in human SRP RNA

Sakamoto, T., Morita, S., Tabata, K., Nakamura, K., Kawai, G.

(2002) J Biochem 132: 177-182

Released	2002-05-22
Method	SOLUTION NMR
Macromolecule	SRP19 binding domain of SRP RNA (nucleic acid)

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1XWP \| pdb_00001xwp	Download File View File

Solution structure of AUCGCA loop

Sakamoto, T., Oguro, A., Kawai, G., Ohtsu, T., Nakamura, Y.

(2005) Nucleic Acids Res 33: 745-754

Released	2005-02-15
Method	SOLUTION NMR
Macromolecule	5'-R(GPGPAPGPAPUPCPGPCPAPCPUPCPCP*A)-3' (nucleic acid)

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1XWU \| pdb_00001xwu	Download File View File

Solution structure of ACAUAGA loop

Sakamoto, T., Oguro, A., Kawai, G., Ohtsu, T., Nakamura, Y.

(2005) Nucleic Acids Res 33: 745-754

Released	2005-02-15
Method	SOLUTION NMR
Macromolecule	5'-R(CPGPAPAPAPCPAPUPAPGPAPUPUPCPGPA)-3' (nucleic acid)

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2F87 \| pdb_00002f87	Download File View File

Solution structure of a GAAG tetraloop in SRP RNA from Pyrococcus furiosus

Okada, K., Takahashi, M., Sakamoto, T., Nakamura, K., Kanai, A., Kawai, G

(2006) Nucleosides Nucleotides Nucleic Acids 25: 383-395

Released	2006-08-08
Method	SOLUTION NMR
Macromolecule	SRP RNA (nucleic acid)

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2FDT \| pdb_00002fdt	Download File View File

Solution structure of a conserved RNA hairpin of eel LINE UnaL2

Nomura, Y., Baba, S., Nakazato, S., Sakamoto, T., Kajikawa, M., Okada, N., Kawai, G.

(2006) Nucleic Acids Res 34: 5184-5193

Released	2006-12-05
Method	SOLUTION NMR
Macromolecule	36-mer (nucleic acid)

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2FYH \| pdb_00002fyh	Download File View File

Solution structure of the 2'-5' RNA ligase-like protein from Pyrococcus furiosus

Okada, K., Matsuda, T., Sakamoto, T., Muto, Y., Yokoyama, S., Kanai, A., Kawai, G., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2009) RNA 15: 420-431

Released	2007-02-20
Method	SOLUTION NMR
Organisms	Pyrococcus furiosus DSM 3638
Macromolecule	putative integral membrane transport protein (protein)

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2RRC \| pdb_00002rrc	Download File View File

Solution Structure of RNA aptamer against AML1 Runt domain

Nomura, Y., Fujiwara, K., Chiba, M., Fukunaga, J., Tanaka, Y., Iibuchi, H., Tanaka, T., Nakamura, Y., Kawai, G., Kozu, T., Sakamoto, T.

To be published

Released	2011-06-29
Method	SOLUTION NMR
Macromolecule	5'-R(PGPGPAPCPCPCP(AP7)PCPCPAPCPGPGPCPGPAPGPGPUPCPCPA)-3' (nucleic acid)

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3A71 \| pdb_00003a71	Download File View File

High resolution structure of Penicillium chrysogenum alpha-L-arabinanase

Sogabe, Y.

(2011) Acta Crystallogr D Biol Crystallogr 67: 415-422

Released	2010-09-15
Method	X-RAY DIFFRACTION 1.14 Å
Organisms	Penicillium chrysogenum
Macromolecule	Exo-arabinanase (protein)
Unique Ligands	ACT, MPD

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3A72 \| pdb_00003a72	Download File View File

High resolution structure of Penicillium chrysogenum alpha-L-arabinanase complexed with arabinobiose

Sogabe, Y.

(2011) Acta Crystallogr D Biol Crystallogr 67: 415-422

Released	2010-09-15
Method	X-RAY DIFFRACTION 1.04 Å
Organisms	Penicillium chrysogenum
Macromolecule	Exo-arabinanase (protein)
Unique branched monosaccharides	AHR

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3AGV \| pdb_00003agv	Download File View File

Crystal structure of a human IgG-aptamer complex

Nomura, Y., Sugiyama, S., Sakamoto, T., Miyakawa, S., Adachi, H., Takano, K., Murakami, S., Inoue, T., Mori, Y., Nakamura, Y., Matsumura, H.

(2010) Nucleic Acids Res 38: 7822-7829

Released	2010-11-10
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Homo sapiens
Macromolecule	Ig gamma-1 chain C region (protein) 5'-R(GPGPAPGPGP(UFT)PGP(CFZ)P(UFT)P(CFZ)P(CFZ)PGPAPAPAGPGPAPAP(CFZ)P(UFT)P(CFZ)P(CFZ)PA)-3' (nucleic acid)
Unique Ligands	CA
Unique branched monosaccharides	BMA, FUL, GAL, GLA, MAN, NAG, NDG

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5B5I \| pdb_00005b5i	Download File View File

The crystal structure of a crustacean hyperglycemic hormone precursor from the kuruma prawn

Tsutsui, N., Nagata, K.

(2016) FEBS J 283: 4325-4339

Released	2016-10-19
Method	X-RAY DIFFRACTION 1.599 Å
Organisms	Penaeus japonicus
Macromolecule	Crustacean hyperglycemic hormones 1 (protein)
Unique Ligands	EOH

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5GTH \| pdb_00005gth	Download File View File

Native XFEL structure of photosystem II (dark dataset)

Suga, M., Shen, J.R.

(2017) Nature 543: 131-135

Released	2017-03-15
Method	X-RAY DIFFRACTION 2.5 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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5GTI \| pdb_00005gti	Download File View File

Native XFEL structure of photosystem II (two flash dataset)

Suga, M., Shen, J.R.

(2017) Nature 543: 131-135

Released	2017-03-15
Method	X-RAY DIFFRACTION 2.5 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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5GVQ \| pdb_00005gvq	Download File View File

Solution structure of the first RRM domain of human spliceosomal protein SF3b49

Kuwasako, K., Nameki, N., Tsuda, K., Takahashi, M., Sato, A., Tochio, N., Inoue, M., Terada, T., Kigawa, T., Kobayashi, N., Shirouzu, M., Ito, T., Sakamoto, T., Wakamatsu, K., Guntert, P., Takahashi, S., Yokoyama, S., Muto, Y., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2017) Protein Sci 26: 280-291

Released	2017-04-12
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Splicing factor 3B subunit 4 (protein)

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5WS5 \| pdb_00005ws5	Download File View File

Native XFEL structure of photosystem II (preflash dark dataset)

Suga, M., Shen, J.R.

(2017) Nature 543: 131-135

Released	2017-03-15
Method	X-RAY DIFFRACTION 2.35 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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5WS6 \| pdb_00005ws6	Download File View File

Native XFEL structure of Photosystem II (preflash two-flash dataset

Suga, M., Shen, J.R.

(2017) Nature 543: 131-135

Released	2017-03-15
Method	X-RAY DIFFRACTION 2.35 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, OEY, PHO, PL9, SQD, UNL

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5XQ3 \| pdb_00005xq3	Download File View File

Crystal structure of a PL 26 exo-rhamnogalacturonan lyase from Penicillium chrysogenum

Kunishige, Y., Iwai, M., Tada, T., Nishimura, S., Sakamoto, T.

(2018) FEBS Lett 592: 1378-1388

Released	2018-03-21
Method	X-RAY DIFFRACTION 2.85 Å
Organisms	Penicillium chrysogenum
Macromolecule	Pcrglx protein (protein)
Unique Ligands	CA

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5XQG \| pdb_00005xqg	Download File View File

Crystal structure of a PL 26 exo-rhamnogalacturonan lyase from Penicillium chrysogenum complexed with unsaturated galacturonosyl rhamnose

Kunishige, Y., Iwai, M., Tada, T., Nishimura, S., Sakamoto, T.

(2018) FEBS Lett 592: 1378-1388

Released	2018-03-21
Method	X-RAY DIFFRACTION 2.74 Å
Organisms	Penicillium chrysogenum
Macromolecule	Pcrglx protein (protein)
Unique Ligands	CA
Unique branched monosaccharides	GAD, RAM

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5XQJ \| pdb_00005xqj	Download File View File

Crystal structure of a PL 26 exo-rhamnogalacturonan lyase from Penicillium chrysogenum complexed with unsaturated galacturonosyl rhamnose substituted with galactose

Kunishige, Y., Iwai, M., Tada, T., Nishimura, S., Sakamoto, T.

(2018) FEBS Lett 592: 1378-1388

Released	2018-04-04
Method	X-RAY DIFFRACTION 2.75 Å
Organisms	Penicillium chrysogenum
Macromolecule	Pcrglx protein (protein)
Unique Ligands	CA
Unique branched monosaccharides	GAD, GAL, RAM

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5XQO \| pdb_00005xqo	Download File View File

Crystal structure of a PL 26 exo-rhamnogalacturonan lyase from Penicillium chrysogenum complexed with tetrameric substrate

Kunishige, Y., Iwai, M., Tada, T., Nishimura, S., Sakamoto, T.

(2018) FEBS Lett 592: 1378-1388

Released	2018-03-21
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Penicillium chrysogenum
Macromolecule	Pcrglx protein (protein)
Unique Ligands	CA
Unique branched monosaccharides	ADA, GAD, RAM

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5Y6T \| pdb_00005y6t	Download File View File

Crystal structure of endo-1,4-beta-mannanase from Eisenia fetida

Hirano, Y., Ueda, M., Tamada, T.

(2018) Enzyme Microb Technol 117: 15-22

Released	2018-06-27
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Eisenia fetida
Macromolecule	endo-1,4-beta-mannanase (protein)
Unique Ligands	IPA, TRS

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6IIE \| pdb_00006iie	Download File View File

Crystal structure of human diacylglycerol kinase alpha EF-hand domains bound to Ca2+

Takahashi, D., Suzuki, K., Sakamoto, T., Iwamoto, T., Murata, T., Sakane, F.

(2019) Protein Sci 28: 694-706

Released	2019-02-20
Method	X-RAY DIFFRACTION 2.142 Å
Organisms	Homo sapiens
Macromolecule	Diacylglycerol kinase alpha (protein)
Unique Ligands	CA, GOL, PG4

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6IK5 \| pdb_00006ik5	Download File View File

Crystal structure of tomato beta-galactosidase (TBG) 4 in complex with galactose

Matsuyama, K., Nakae, S., Igarashi, K., Tada, T., Ishimaru, M.

(2020) Planta 252: 72-72

Released	2018-11-28
Method	X-RAY DIFFRACTION 1.82 Å
Organisms	Solanum lycopersicum
Macromolecule	Beta-galactosidase (protein)
Unique Ligands	GAL, NAG
Unique branched monosaccharides	NAG

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6IK6 \| pdb_00006ik6	Download File View File

Crystal structure of Tomato beta-galactosidase (TBG) 4 with beta-1,4-galactobiose

Matsuyama, K., Nakae, S., Igarashi, K., Tada, T., Ishimaru, M.

(2020) Planta 252: 72-72

Released	2018-11-28
Method	X-RAY DIFFRACTION 2.791 Å
Organisms	Solanum lycopersicum
Macromolecule	Beta-galactosidase (protein)
Unique Ligands	CL, NAG
Unique branched monosaccharides	GAL, NAG

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6IK7 \| pdb_00006ik7	Download File View File

Crystal structure of tomato beta-galactosidase (TBG) 4 in complex with beta-1,3-galactobiose

Matsuyama, K., Nakae, S., Igarashi, K., Tada, T., Ishimaru, M.

(2020) Planta 252: 72-72

Released	2018-11-28
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Solanum lycopersicum
Macromolecule	Beta-galactosidase (protein)
Unique Ligands	NAG
Unique branched monosaccharides	GAL, NAG

1 to 25 of 40 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

1L1W | pdb_00001l1w

1XWP | pdb_00001xwp

1XWU | pdb_00001xwu

2F87 | pdb_00002f87

2FDT | pdb_00002fdt

2FYH | pdb_00002fyh

2RRC | pdb_00002rrc

3A71 | pdb_00003a71

3A72 | pdb_00003a72

3AGV | pdb_00003agv

5B5I | pdb_00005b5i

5GTH | pdb_00005gth

5GTI | pdb_00005gti

5GVQ | pdb_00005gvq

5WS5 | pdb_00005ws5

5WS6 | pdb_00005ws6

5XQ3 | pdb_00005xq3

5XQG | pdb_00005xqg

5XQJ | pdb_00005xqj

5XQO | pdb_00005xqo

5Y6T | pdb_00005y6t

6IIE | pdb_00006iie

6IK5 | pdb_00006ik5

6IK6 | pdb_00006ik6

6IK7 | pdb_00006ik7