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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Aihara, H."

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Search Summary

This query matches 149 Structures.

Refinements

Structure Determination Methodology

experimental (149)

Scientific Name of Source Organism

	Homo sapiens (55)
	Severe acute respiratory syndrome coronavirus 2 (15)
	Methylosinus trichosporium OB3b (12)
	Agrobacterium fabrum str. C58 (9)
	synthetic construct (9)
	Moorella thermoacetica ATCC 39073 (8)
	Tequatrovirus T4 (6)
	Camelidae (5)
	Lambdavirus lambda (4)
	Pyrococcus furiosus (4)

More...

Taxonomy

	Eukaryota (75)
	Bacteria (46)
	Riboviria (25)
	Duplodnaviria (11)
	other sequences (9)
	Archaea (5)
	Varidnaviria (2)
	Monodnaviria (1)

Experimental Method

	X-RAY DIFFRACTION (142)
	ELECTRON MICROSCOPY (5)
	SOLUTION NMR (2)

Polymer Entity Type

	Protein (149)
	DNA (40)
	RNA (2)

Refinement Resolution (Å)

	1.0 - 1.5 (11)
	1.5 - 2.0 (57)
	2.0 - 2.5 (36)
	2.5 - 3.0 (19)
	3.0 - 3.5 (19)
	3.5 - 4.0 (4)
	4.0 - 4.5 (1)

Release Date

	1995 - 1999 (2)
	2000 - 2004 (1)
	2005 - 2009 (4)
	2010 - 2014 (19)
	2015 - 2019 (40)
	2020 - 2024 (81)
	2025 - 2029 (2)

Enzyme Classification Name

	Hydrolases (66)
	Transferases (15)
	Oxidoreductases (13)
	Ligases (3)
	Lyases (3)

Membrane Protein Annotation

mpstruc (1)

Symmetry Type

	Asymmetric (92)
	Cyclic (49)
	Dihedral (9)

SCOP Classification

	Alpha and beta proteins (a+b) (21)
	All alpha proteins (13)
	Artifacts (22)
	Alpha and beta proteins (a/b) (19)
	All beta proteins (2)
	Small proteins (2)

AllSelected

1 to 25 of 149 Structures

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1AA3 \| pdb_00001aa3	Download File View File

C-TERMINAL DOMAIN OF THE E. COLI RECA, NMR, MINIMIZED AVERAGE STRUCTURE

Aihara, H., Ito, Y., Kurumizaka, H., Terada, T., Yokoyama, S., Shibata, T., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(1997) J Mol Biology 274: 213-221

Released	1997-07-23
Method	SOLUTION NMR
Organisms	Escherichia coli K-12
Macromolecule	RECA (protein)

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1B22 \| pdb_00001b22	Download File View File

RAD51 (N-TERMINAL DOMAIN)

Aihara, H., Ito, Y., Kurumizaka, H., Yokoyama, S., Shibata, T., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(1999) J Mol Biology 290: 495-504

Released	1999-12-03
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	DNA REPAIR PROTEIN RAD51 (protein)

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1P7D \| pdb_00001p7d	Download File View File

Crystal structure of the Lambda Integrase (residues 75-356) bound to DNA

Aihara, H., Kwon, H.J., Nunes-Duby, S.E., Landy, A., Ellenberger, T.

(2003) Mol Cell 12: 187-198

Released	2003-08-12
Method	X-RAY DIFFRACTION 2.95 Å
Organisms	Lambdavirus lambda
Macromolecule	Integrase (protein) 26-MER (nucleic acid) 5'-D(CPAPAPTPGPCPCPAPAPCPTPTP*T)-3' (nucleic acid)

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1Z19 \| pdb_00001z19	Download File View File

Crystal structure of a lambda integrase(75-356) dimer bound to a COC' core site

Biswas, T., Aihara, H., Radman-Livaja, M., Filman, D., Landy, A., Ellenberger, T.

(2005) Nature 435: 1059-1066

Released	2005-06-28
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Lambdavirus lambda
Macromolecule	Integrase (protein) 33-MER (nucleic acid) 5'-D(CPTPCPGPTPTPCPAPGPCPTPTPTPTPTPT)-3' (nucleic acid) 5'-D(PTPTPTPAPTPAPCPTPAPAPGPTPTPGPGPCPAPTPTPA)-3' (nucleic acid)

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1Z1B \| pdb_00001z1b	Download File View File

Crystal structure of a lambda integrase dimer bound to a COC' core site

Biswas, T., Aihara, H., Radman-Livaja, M., Filman, D., Landy, A., Ellenberger, T.

(2005) Nature 435: 1059-1066

Released	2005-06-28
Method	X-RAY DIFFRACTION 3.8 Å
Organisms	Lambdavirus lambda
Macromolecule	Unique protein chains: 1 Unique nucleic acid chains: 5

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1Z1G \| pdb_00001z1g	Download File View File

Crystal structure of a lambda integrase tetramer bound to a Holliday junction

Biswas, T., Aihara, H., Radman-Livaja, M., Filman, D., Landy, A., Ellenberger, T.

(2005) Nature 435: 1059-1066

Released	2005-06-28
Method	X-RAY DIFFRACTION 4.4 Å
Organisms	Lambdavirus lambda
Macromolecule	Unique protein chains: 1 Unique nucleic acid chains: 6

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2V6E \| pdb_00002v6e	Download File View File

protelomerase TelK complexed with substrate DNA

Aihara, H., Huang, W.M., Ellenberger, T.

(2007) Mol Cell 27: 901

Released	2007-10-02
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Klebsiella phage phiKO2 Ravinvirus N15
Macromolecule	PROTELEMORASE (protein) TELRL (nucleic acid)
Unique Ligands	VO4

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4DWP \| pdb_00004dwp	Download File View File

SeMet protelomerase tela covalently complexed with substrate DNA

Shi, K., Aihara, H.

(2013) PLoS Biol 11: e1001472-e1001472

Released	2013-02-13
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	Agrobacterium fabrum str. C58
Macromolecule	Protelomerase (protein) DNA (5'-D(CPAPTPGPAPTPAPTPTPGPTPTPAPTPTPGPTPAPA)-3') (nucleic acid) DNA (5'-D(TPTPAPCPAPAPTPAPAPCPAPAPTPAPT)-3') (nucleic acid)
Unique Ligands	TMP

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4E0G \| pdb_00004e0g	Download File View File

Protelomerase tela/DNA hairpin product/vanadate complex

Shi, K., Aihara, H.

(2013) PLoS Biol 11: e1001472-e1001472

Released	2013-02-13
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Agrobacterium fabrum str. C58
Macromolecule	Protelomerase (protein) DNA (5'-D(CPAPTPAPAPTPAPAPCPAPAPTPA)-3') (nucleic acid) DNA (5'-D(TPCPAPTPGPAPTPAPTPTPGPTPTPAPTPTPAPTPG)-3') (nucleic acid)
Unique Ligands	VO4

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4E0J \| pdb_00004e0j	Download File View File

Protelomerase tela R255A mutant complexed with DNA hairpin product

Shi, K., Aihara, H.

(2013) PLoS Biol 11: e1001472-e1001472

Released	2013-02-13
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Agrobacterium fabrum str. C58
Macromolecule	Protelomerase (protein) DNA (5'-D(CPAPTPAPAPTPAPAPCPAPAPTPA)-3') (nucleic acid) DNA (5'-D(TPCPAPTPGPAPTPAPTPTPGPTPTPAPTPTPAPTPG)-3') (nucleic acid)
Unique Ligands	CL, NA

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4E0P \| pdb_00004e0p	Download File View File

Protelomerase tela covalently complexed with substrate DNA

Shi, K., Aihara, H.

(2013) PLoS Biol 11: e1001472-e1001472

Released	2013-02-13
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Agrobacterium fabrum str. C58
Macromolecule	Protelomerase (protein) DNA (5'-D(CPAPTPAPAPTPAPAPCPAPAPTPAPT)-3') (nucleic acid) DNA (5'-D(CPAPTPGPAPTPAPTPTPGPTPTPAPTPTPAPTPG)-3') (nucleic acid)
Unique Ligands	EDO, TMP

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4E0Y \| pdb_00004e0y	Download File View File

Protelomerase tela covalently complexed with mutated substrate DNA

Shi, K., Aihara, H.

(2013) PLoS Biol 11: e1001472-e1001472

Released	2013-02-13
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Agrobacterium fabrum str. C58
Macromolecule	Protelomerase (protein) DNA (5'-D(CPAPTPAPAPTPAPAPCPAPAPTPAPT)-3') (nucleic acid) DNA (5'-D(CPCPAPTPGPAPTPAPTPTPGPTPTPAPTPTPAPTP*G)-3') (nucleic acid)
Unique Ligands	GOL, TMP

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4E0Z \| pdb_00004e0z	Download File View File

Protelomerase tela R205A covalently complexed with substrate DNA

Shi, K., Aihara, H.

(2013) PLoS Biol 11: e1001472-e1001472

Released	2013-02-13
Method	X-RAY DIFFRACTION 2.42 Å
Organisms	Agrobacterium fabrum str. C58
Macromolecule	Protelomerase (protein) DNA (5'-D(CPAPTPAPAPTPAPAPCPAPAPTPA)-3') (nucleic acid) DNA (5'-D(TPCPATPGPAPTPAPTPTPGPTPTPAPTPTPAPTPG)-3') (nucleic acid)
Unique Ligands	GOL, TMP

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4E10 \| pdb_00004e10	Download File View File

Protelomerase tela Y201A covalently complexed with substrate DNA

Shi, K., Aihara, H.

(2013) PLoS Biol 11: e1001472-e1001472

Released	2013-02-13
Method	X-RAY DIFFRACTION 2.506 Å
Organisms	Agrobacterium fabrum str. C58
Macromolecule	Protelomerase (protein) DNA (5'-D(CPAPTPAPAP(BRU)PAPAPCPAPAP(BRU)PAPT)-3') (nucleic acid) DNA (5'-D(CPAPTPGPAPTPAP(BRU)P(BRU)PGP(BRU)P(BRU)PAP(BRU)P(BRU)PAP(BRU)PG)-3') (nucleic acid)
Unique Ligands	TMP

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4EP4 \| pdb_00004ep4	Download File View File

Thermus thermophilus RuvC structure

Chen, L., Shi, K., Yin, Z.Q., Aihara, H.

(2013) Nucleic Acids Res 41: 648-656

Released	2012-11-14
Method	X-RAY DIFFRACTION 1.28 Å
Organisms	Thermus thermophilus HB8
Macromolecule	Crossover junction endodeoxyribonuclease RuvC (protein)
Unique Ligands	GOL, MG

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4EP5 \| pdb_00004ep5	Download File View File

Thermus thermophilus RuvC structure

Chen, L., Shi, K., Yin, Z.Q., Aihara, H.

(2013) Nucleic Acids Res 41: 648-656

Released	2012-11-14
Method	X-RAY DIFFRACTION 2.08 Å
Organisms	Thermus thermophilus HB8
Macromolecule	Crossover junction endodeoxyribonuclease RuvC (protein)
Unique Ligands	GOL, SO4

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4F1H \| pdb_00004f1h	Download File View File

Crystal structure of TDP2 from Danio rerio complexed with a single strand DNA

Shi, K., Kurahashi, K., Aihara, H.

(2012) Nat Struct Mol Biol 19: 1372-1377

Released	2012-10-31
Method	X-RAY DIFFRACTION 1.662 Å
Organisms	Danio rerio
Macromolecule	Tyrosyl-DNA phosphodiesterase 2 (protein) DNA (5'-D(PTPGPCPAP*G)-3') (nucleic acid)
Unique Ligands	GOL, MG, PO4

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4F1I \| pdb_00004f1i	Download File View File

Crystal structure of SeMet TDP2 from Caenorhabditis elegans

Shi, K., Kurahashi, K., Aihara, H.

(2012) Nat Struct Mol Biol 19: 1372-1377

Released	2012-10-31
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Caenorhabditis elegans
Macromolecule	5'-tyrosyl-DNA phosphodiesterase (protein)
Unique Ligands	GOL

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4F41 \| pdb_00004f41	Download File View File

Protelomerase TelA mutant R255A complexed with CTTG hairpin DNA

Shi, K., Aihara, H.

(2012) J Biological Chem 287: 25551-25563

Released	2012-06-13
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Agrobacterium fabrum str. C58
Macromolecule	Protelomerase (protein) DNA hairpin (nucleic acid)

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4F43 \| pdb_00004f43	Download File View File

Protelomerase TelA mutant R255A complexed with CAAG hairpin DNA

Shi, K., Aihara, H.

(2012) J Biological Chem 287: 25551-25563

Released	2012-06-13
Method	X-RAY DIFFRACTION 2.354 Å
Organisms	Agrobacterium fabrum str. C58
Macromolecule	Protelomerase (protein) DNA hairpin (nucleic acid)

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4FPV \| pdb_00004fpv	Download File View File

Crystal structure of D. rerio TDP2 complexed with single strand DNA product

Shi, K., Kurahashi, K., Aihara, H.

(2012) Nat Struct Mol Biol 19: 1372-1377

Released	2012-10-31
Method	X-RAY DIFFRACTION 1.73 Å
Organisms	Danio rerio
Macromolecule	Tyrosyl-DNA phosphodiesterase 2 (protein) DNA (5'-D(PTPGPCPAP*G)-3') (nucleic acid)
Unique Ligands	GOL, MG, NA

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4FVA \| pdb_00004fva	Download File View File

Crystal structure of truncated Caenorhabditis elegans TDP2

Shi, K., Kurahashi, K., Aihara, H.

(2012) Nat Struct Mol Biol 19: 1372-1377

Released	2012-10-31
Method	X-RAY DIFFRACTION 2.07 Å
Organisms	Caenorhabditis elegans
Macromolecule	5'-tyrosyl-DNA phosphodiesterase (protein)
Unique Ligands	EDO, MG, MLI

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4FW1 \| pdb_00004fw1	Download File View File

Crystal structure of two-domain RSV INTEGRASE covalently linked with DNA

Shi, K., Aihara, H.

(2013) PLoS One 8: e56892-e56892

Released	2013-05-15
Method	X-RAY DIFFRACTION 1.86 Å
Organisms	Rous sarcoma virus - Prague C
Macromolecule	Integrase (protein)

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4FW2 \| pdb_00004fw2	Download File View File

Crystal structure of RSV three-domain integrase with disordered N-terminal domain

Shi, K., Aihara, H.

(2013) PLoS One 8: e56892-e56892

Released	2013-05-15
Method	X-RAY DIFFRACTION 2.65 Å
Organisms	Rous sarcoma virus - Prague C
Macromolecule	Integrase (protein)

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4GEW \| pdb_00004gew	Download File View File

Crystal structure of TDP2 from C. elegans

Shi, K., Kurahashi, K., Aihara, H.

(2012) Nat Struct Mol Biol 19: 1372-1377

Released	2012-10-31
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	Caenorhabditis elegans
Macromolecule	5'-tyrosyl-DNA phosphodiesterase (protein)
Unique Ligands	GOL

1 to 25 of 149 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

1AA3 | pdb_00001aa3

1B22 | pdb_00001b22

1P7D | pdb_00001p7d

1Z19 | pdb_00001z19

1Z1B | pdb_00001z1b

1Z1G | pdb_00001z1g

2V6E | pdb_00002v6e

4DWP | pdb_00004dwp

4E0G | pdb_00004e0g

4E0J | pdb_00004e0j

4E0P | pdb_00004e0p

4E0Y | pdb_00004e0y

4E0Z | pdb_00004e0z

4E10 | pdb_00004e10

4EP4 | pdb_00004ep4

4EP5 | pdb_00004ep5

4F1H | pdb_00004f1h

4F1I | pdb_00004f1i

4F41 | pdb_00004f41

4F43 | pdb_00004f43

4FPV | pdb_00004fpv

4FVA | pdb_00004fva

4FW1 | pdb_00004fw1

4FW2 | pdb_00004fw2

4GEW | pdb_00004gew