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232,418 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Ishikawa, H."

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Search Summary

This query matches 20 Structures.

Refinements

Structure Determination Methodology

experimental (20)

Scientific Name of Source Organism

	Thermus thermophilus HB8 (10)
	HIV-1 06TG.HT008 (3)
	Thermus thermophilus (3)
	Pyrococcus horikoshii OT3 (2)
	Geobacillus kaustophilus (1)
	Sulfurisphaera tokodaii str. 7 (1)

Taxonomy

	Bacteria (14)
	Archaea (3)
	Riboviria (3)

Experimental Method

X-RAY DIFFRACTION (20)

Polymer Entity Type

	Protein (20)
	RNA (3)

Refinement Resolution (Å)

	1.0 - 1.5 (1)
	1.5 - 2.0 (4)
	2.0 - 2.5 (6)
	2.5 - 3.0 (9)

Release Date

	2005 - 2009 (8)
	2010 - 2014 (9)
	2020 - 2024 (3)

Enzyme Classification Name

	Hydrolases (15)
	Transferases (4)
	Lyases (1)

Symmetry Type

	Asymmetric (17)
	Cyclic (3)

SCOP Classification

	Alpha and beta proteins (a+b) (8)
	Alpha and beta proteins (a/b) (2)

AllSelected

1 to 20 of 20 Structures

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2ZIE	Download File View File

Crystal Structure of TTHA0409, Putatative DNA Modification Methylase from Thermus thermophilus HB8- Selenomethionine derivative

Morita, R., Ishikawa, H., Nakagawa, N., Masui, R., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2008) Proteins 73: 259-264

Released	2008-07-29
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Thermus thermophilus
Macromolecule	Putative modification methylase (protein)

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2ZIF	Download File View File

Crystal Structure of TTHA0409, Putative DNA Modification Methylase from Thermus thermophilus HB8- Complexed with S-Adenosyl-L-Methionine

Morita, R., Ishikawa, H., Nakagawa, N., Masui, R., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2008) Proteins 73: 259-264

Released	2008-07-29
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Thermus thermophilus
Macromolecule	Putative modification methylase (protein)
Unique Ligands	SAM

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2ZIG	Download File View File

Crystal Structure of TTHA0409, Putative DNA Modification Methylase from Thermus thermophilus HB8

Morita, R., Ishikawa, H., Nakagawa, N., Masui, R., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2008) Proteins 73: 259-264

Released	2008-07-29
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Thermus thermophilus
Macromolecule	Putative modification methylase (protein)

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3A4Y	Download File View File

Crystal Structure of H61A mutant TTHA0252 from Thermus thermophilus HB8

Ishikawa, H., Nakagawa, N., Kuramitsu, S., Yokoyama, S., Masui, R., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2009-08-04
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Thermus thermophilus HB8
Macromolecule	Ribonuclease TTHA0252 (protein)
Unique Ligands	FLC, SO4, ZN

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3AAL	Download File View File

Crystal Structure of endonuclease IV from Geobacillus kaustophilus

Asano, R., Ishikawa, H., Nakane, S., Nakagawa, N., Kuramitsu, S., Masui, R., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2011) Acta Crystallogr D Biol Crystallogr 67: 149-155

Released	2010-12-01
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Geobacillus kaustophilus
Macromolecule	Probable endonuclease 4 (protein)
Unique Ligands	CAC, FE, ZN

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3AAM	Download File View File

Crystal structure of endonuclease IV from Thermus thermophilus HB8

Asano, R., Ishikawa, H., Nakane, S., Baba, S., Nakagawa, N., Kuramitsu, S., Masui, R., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2011) Acta Crystallogr D Biol Crystallogr 67: 149-155

Released	2010-12-01
Method	X-RAY DIFFRACTION 1.58 Å
Organisms	Thermus thermophilus HB8
Macromolecule	Endonuclease IV (protein)
Unique Ligands	MN, PO4

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3ADR	Download File View File

The first crystal structure of an archaeal metallo-beta-lactamase superfamily protein; ST1585 from Sulfolobus tokodaii

Shimada, A., Ishikawa, H., Nakagawa, N., Kuramitsu, S., Masui, R.

(2010) Proteins 78: 2399-2402

Released	2010-04-21
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Sulfurisphaera tokodaii str. 7
Macromolecule	Putative uncharacterized protein ST1585 (protein)
Unique Ligands	EDO, EPE, ZN

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3AF5	Download File View File

The crystal structure of an archaeal CPSF subunit, PH1404 from Pyrococcus horikoshii

Nishida, Y., Ishikawa, H., Nakagawa, N., Masui, R., Kuramitsu, S.

(2010) Proteins 78: 2395-2398

Released	2010-04-21
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Pyrococcus horikoshii OT3
Macromolecule	Putative uncharacterized protein PH1404 (protein)
Unique Ligands	ACY, SO4, ZN

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3AF6	Download File View File

The crystal structure of an archaeal CPSF subunit, PH1404 from Pyrococcus horikoshii complexed with RNA-analog

Nishida, Y., Ishikawa, H., Nakagawa, N., Masui, R., Kuramitsu, S.

(2010) Proteins 78: 2395-2398

Released	2010-04-21
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Pyrococcus horikoshii OT3
Macromolecule	Putative uncharacterized protein PH1404 (protein) 5'-R((SSU)P(SSU)P(SSU)P(SSU)P(SSU)P(SSU))-3' (nucleic acid)
Unique Ligands	SO4, ZN

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3AU2	Download File View File

DNA polymerase X from Thermus thermophilus HB8 complexed with Ca-dGTP

Nakane, S., Ishikawa, H., Wakamatsu, T., Nakagawa, N., Masui, R., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2012) J Mol Biol 417: 179-196

Released	2012-01-25
Method	X-RAY DIFFRACTION 1.4 Å
Organisms	Thermus thermophilus HB8
Macromolecule	DNA polymerase beta family (X family) (protein)
Unique Ligands	CA, CL, DGT, ZN

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3IDZ	Download File View File

Crystal Structure of S378Q mutant TTHA0252 from Thermus thermophilus HB8

Ishikawa, H., Nakagawa, N., Kuramitsu, S., Yokoyama, S., Masui, R., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2009-08-04
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Thermus thermophilus HB8
Macromolecule	Ribonuclease TTHA0252 (protein)
Unique Ligands	FLC, SO4, ZN

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3IE0	Download File View File

Crystal Structure of S378Y mutant TTHA0252 from Thermus thermophilus HB8

Ishikawa, H., Nakagawa, N., Kuramitsu, S., Yokoyama, S., Masui, R., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2009-08-04
Method	X-RAY DIFFRACTION 2.73 Å
Organisms	Thermus thermophilus HB8
Macromolecule	Ribonuclease TTHA0252 (protein)
Unique Ligands	FLC, SO4, ZN

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3IE1	Download File View File

Crystal structure of H380A mutant TTHA0252 from Thermus thermophilus HB8 complexed with RNA

Ishikawa, H., Nakagawa, N., Kuramitsu, S., Yokoyama, S., Masui, R., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2009-08-04
Method	X-RAY DIFFRACTION 2.85 Å
Organisms	Thermus thermophilus HB8
Macromolecule	Ribonuclease TTHA0252 (protein) RNA (5'-R(PUPUPUPU)-3') (nucleic acid)
Unique Ligands	FLC, SO4, ZN

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3IE2	Download File View File

Crystal Structure of H400V mutant TTHA0252 from Thermus thermophilus HB8

Ishikawa, H., Nakagawa, N., Kuramitsu, S., Yokoyama, S., Masui, R., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2009-08-04
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Thermus thermophilus HB8
Macromolecule	Ribonuclease TTHA0252 (protein)
Unique Ligands	BTB, SO4, ZN

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3IEK	Download File View File

Crystal Structure of native TTHA0252 from Thermus thermophilus HB8

Ishikawa, H., Nakagawa, N., Kuramitsu, S., Yokoyama, S., Masui, R.

To be published

Released	2010-07-28
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Thermus thermophilus HB8
Macromolecule	Ribonuclease TTHA0252 (protein)
Unique Ligands	FLC, SO4, ZN

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3IEL	Download File View File

Crystal Structure of TTHA0252 from Thermus thermophilus HB8 complexed with UMP

Ishikawa, H., Nakagawa, N., Kuramitsu, S., Yokoyama, S., Masui, R.

To be published

Released	2010-07-28
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	Thermus thermophilus HB8
Macromolecule	Ribonuclease TTHA0252 (protein)
Unique Ligands	FLC, SO4, U5P, ZN

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3IEM	Download File View File

Crystal Structure of TTHA0252 from Thermus thermophilus HB8 complexed with RNA analog

Ishikawa, H., Nakagawa, N., Kuramitus, S., Yokoyama, S., Masui, R.

To be published

Released	2010-07-28
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Thermus thermophilus HB8
Macromolecule	Ribonuclease TTHA0252 (protein) RNA (5'-R((SSU)P(SSU)P(SSU)P(SSU)P(SSU)P(SSU))-3') (nucleic acid)
Unique Ligands	FLC, SO4, ZN

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8JYH	Download File View File

Crystal structure of engineered HIV-1 Reverse Transcriptase RNase H domain complexed with laccaic acid C

Ito, Y., Lu, H., Kitajima, M., Ishikawa, H., Nakata, Y., Iwatani, Y., Hoshino, T.

(2023) J Nat Prod 86: 2487-2495

Released	2023-08-16
Method	X-RAY DIFFRACTION 2.21 Å
Organisms	HIV-1 06TG.HT008
Macromolecule	Pol protein,Pol protein,HIV-1 Reverse Transcriptase RNase H active domain (protein)
Unique Ligands	MN, V96, ZN

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8JYI	Download File View File

Crystal structure of engineered HIV-1 Reverse Transcriptase RNase H domain complexed with laccaic acid E

Ito, Y., Lu, H., Kitajima, M., Ishikawa, H., Nakata, Y., Iwatani, Y., Hoshino, T.

(2023) J Nat Prod 86: 2487-2495

Released	2023-08-16
Method	X-RAY DIFFRACTION 1.92 Å
Organisms	HIV-1 06TG.HT008
Macromolecule	Pol protein,Pol protein,Ribonuclease H (protein)
Unique Ligands	MN, V9O, ZN

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8JYJ	Download File View File

Crystal structure of engineered HIV-1 Reverse Transcriptase RNase H domain complexed with laccaic acid A

Ito, Y., Lu, H., Kitajima, M., Ishikawa, H., Nakata, Y., Iwatani, Y., Hoshino, T.

(2023) J Nat Prod 86: 2487-2495

Released	2023-08-16
Method	X-RAY DIFFRACTION 2.01 Å
Organisms	HIV-1 06TG.HT008
Macromolecule	Pol protein,Pol protein,HIV-1 Reverse Transcriptase RNase H active domain (protein)
Unique Ligands	MN, VA9, ZN

1 to 20 of 20 Structures

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