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234,136 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Nishio, M."

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Search Summary

This query matches 21 Structures.

Refinements

Structure Determination Methodology

experimental (21)

Scientific Name of Source Organism

	Homo sapiens (10)
	Sulfurisphaera tokodaii (7)
	Thermus thermophilus HB8 (2)
	Pyrococcus horikoshii (1)
	Sulfurisphaera tokodaii str. 7 (1)

Taxonomy

	Eukaryota (10)
	Archaea (9)
	Bacteria (2)

Experimental Method

X-RAY DIFFRACTION (21)

Polymer Entity Type

	Protein (21)
	DNA (1)

Refinement Resolution (Å)

	1.5 - 2.0 (6)
	2.0 - 2.5 (10)
	2.5 - 3.0 (3)
	3.0 - 3.5 (2)

Release Date

	2005 - 2009 (11)
	2010 - 2014 (2)
	2015 - 2019 (4)
	2020 - 2024 (4)

Enzyme Classification Name

	Hydrolases (4)
	Oxidoreductases (2)
	Transferases (2)

Symmetry Type

	Asymmetric (12)
	Cyclic (8)
	Dihedral (2)

SCOP Classification

	All beta proteins (5)
	Alpha and beta proteins (a/b) (3)
	Alpha and beta proteins (a+b) (1)

AllSelected

1 to 21 of 21 Structures

Page 1 of 1

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1VFF \| pdb_00001vff	Download File View File

beta-glycosidase from Pyrococcus horikoshii

Akiba, T., Nishio, M., Matsui, I., Harata, K.

(2004) Proteins 57: 422-431

Released	2005-03-29
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Pyrococcus horikoshii
Macromolecule	beta-glucosidase (protein)

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2EB7 \| pdb_00002eb7	Download File View File

Crystal structure of the hypothetical regulator from Sulfolobus tokodaii 7

Kumarevel, T.S., Nishio, M., Shinkai, A., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2008) J Struct Biol 161: 9-17

Released	2007-11-06
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Sulfurisphaera tokodaii str. 7
Macromolecule	146aa long hypothetical transcriptional regulator (protein)

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2J40 \| pdb_00002j40	Download File View File

1-pyrroline-5-carboxylate dehydrogenase from Thermus thermophilus with bound inhibitor L-proline and NAD.

Inagaki, E., Sakamoto, K., Nishio, M., Yokoyama, S.

To be published

Released	2007-10-02
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Thermus thermophilus HB8
Macromolecule	1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE (protein)
Unique Ligands	ACT, MPD, MRD, NA, NAD, PRO

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2J5N \| pdb_00002j5n	Download File View File

1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE FROM THERMUS THERMOPHIRUS WITH BOUND INHIBITOR GLYCINE AND NAD.

Inagaki, E., Sakamoto, K., Nishio, M., Yokoyama, S.

To be published

Released	2007-10-16
Method	X-RAY DIFFRACTION 1.63 Å
Organisms	Thermus thermophilus HB8
Macromolecule	1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE (protein)
Unique Ligands	ACT, GLY, MPD, MRD, NA, NAD

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2YR2 \| pdb_00002yr2	Download File View File

Crystal Structure of the Hypothetical regulator from Sulfolobus tokodaii

Kumarevel, T.S., Tanaka, T., Nishio, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2007-10-02
Method	X-RAY DIFFRACTION 2.01 Å
Organisms	Sulfurisphaera tokodaii
Macromolecule	146aa long hypothetical transcriptional regulator (protein)
Unique Ligands	ZN

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3A4U \| pdb_00003a4u	Download File View File

Crystal structure of MCFD2 in complex with carbohydrate recognition domain of ERGIC-53

Nishio, M., Kamiya, Y., Mizushima, T., Wakatsuki, S., Sasakawa, H., Yamamoto, K., Uchiyama, S., Noda, M., McKay, A.R., Fukui, K., Hauri, H.P., Kato, K.

(2010) Proc Natl Acad Sci U S A 107: 4034-4039

Released	2010-01-05
Method	X-RAY DIFFRACTION 1.84 Å
Organisms	Homo sapiens
Macromolecule	Multiple coagulation factor deficiency protein 2 (protein) Protein ERGIC-53 (protein)
Unique Ligands	CA, GOL

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3GEZ \| pdb_00003gez	Download File View File

Crystal Structure of the hypothetical egulator from Sulfolobus tokodaii 7

Kumarevel, T., Tanaka, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2009) Nucleic Acids Res 37: 4723-4735

Released	2009-08-25
Method	X-RAY DIFFRACTION 2 Å
Organisms	Sulfurisphaera tokodaii
Macromolecule	146aa long hypothetical transcriptional regulator (protein)
Unique Ligands	CA

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3GF2 \| pdb_00003gf2	Download File View File

Crystal structure of the hypothetical regulator ST1710 complexed with sodium salicylate

Kumarevel, T., Tanaka, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2009) Nucleic Acids Res 37: 4723-4735

Released	2009-08-25
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Sulfurisphaera tokodaii
Macromolecule	146aa long hypothetical transcriptional regulator (protein)
Unique Ligands	SAL

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3GFI \| pdb_00003gfi	Download File View File

Crystal structure of ST1710 complexed with its promoter DNA

Kumarevel, T., Tanaka, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2009) Nucleic Acids Res 37: 4723-4735

Released	2009-08-25
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Sulfurisphaera tokodaii
Macromolecule	146aa long hypothetical transcriptional regulator (protein) 5'-D(TPAPAPCPAPAPTPAPGPCPAPAPA)-3' (nucleic acid) 5'-D(TPTPGPCPTPAPTPTPGP*T)-3' (nucleic acid)

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3GFJ \| pdb_00003gfj	Download File View File

Crystal structure of the ST1710 mutant (R89A) protein

Kumarevel, T., Tanaka, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2009) Nucleic Acids Res 37: 4723-4735

Released	2009-08-25
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Sulfurisphaera tokodaii
Macromolecule	146aa long hypothetical transcriptional regulator (protein)
Unique Ligands	CA

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3GFL \| pdb_00003gfl	Download File View File

Crystal structure of the ST1710 mutant (R90A) protein

Kumarevel, T., Tanaka, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2009) Nucleic Acids Res 37: 4723-4735

Released	2009-08-25
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Sulfurisphaera tokodaii
Macromolecule	146aa long hypothetical transcriptional regulator (protein)
Unique Ligands	CA

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3GFM \| pdb_00003gfm	Download File View File

Crystal structure of the ST1710 mutant (K91A) protein

Kumarevel, T., Tanaka, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2009) Nucleic Acids Res 37: 4723-4735

Released	2009-08-25
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Sulfurisphaera tokodaii
Macromolecule	146aa long hypothetical transcriptional regulator (protein)
Unique Ligands	CA

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4MKC \| pdb_00004mkc	Download File View File

Crystal Structure of Anaplastic Lymphoma Kinase Complexed with LDK378

Lee, C.C., Spraggon, G.

(2014) Cancer Discov 4: 662-673

Released	2014-04-09
Method	X-RAY DIFFRACTION 2.01 Å
Organisms	Homo sapiens
Macromolecule	ALK tyrosine kinase receptor (protein)
Unique Ligands	4MK, GOL

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4YGB \| pdb_00004ygb	Download File View File

Crystal structure of ERGIC-53/MCFD2, monoclinic calcium-free form

Satoh, T., Nishio, M., Yagi-Utsumi, M., Suzuki, K., Anzai, T., Mizushima, T., Kamiya, Y., Kato, K.

(2020) Acta Crystallogr F Struct Biol Commun 76: 216-221

Released	2016-04-06
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Homo sapiens
Macromolecule	Multiple coagulation factor deficiency protein 2 (protein) Protein ERGIC-53 (protein)
Unique Ligands	CA, GOL

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4YGC \| pdb_00004ygc	Download File View File

Crystal structure of ERGIC-53/MCFD2, monoclinic calcium-bound form 1

Satoh, T., Nishio, M., Yagi-Utsumi, M., Suzuki, K., Anzai, T., Mizushima, T., Kamiya, Y., Kato, K.

(2020) Acta Crystallogr F Struct Biol Commun 76: 216-221

Released	2016-04-06
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens
Macromolecule	Multiple coagulation factor deficiency protein 2 (protein) Protein ERGIC-53 (protein)
Unique Ligands	CA, CL

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4YGD \| pdb_00004ygd	Download File View File

Crystal structure of ERGIC-53/MCFD2, monoclinic calcium-bound form 2

Satoh, T., Nishio, M., Yagi-Utsumi, M., Suzuki, K., Anzai, T., Mizushima, T., Kamiya, Y., Kato, K.

(2020) Acta Crystallogr F Struct Biol Commun 76: 216-221

Released	2016-04-06
Method	X-RAY DIFFRACTION 2.51 Å
Organisms	Homo sapiens
Macromolecule	Multiple coagulation factor deficiency protein 2 (protein) Protein ERGIC-53 (protein)
Unique Ligands	CA, CL

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4YGE \| pdb_00004yge	Download File View File

Crystal structure of ERGIC-53/MCFD2, trigonal calcium-bound form 2

Satoh, T., Nishio, M., Yagi-Utsumi, M., Suzuki, K., Anzai, T., Mizushima, T., Kamiya, Y., Kato, K.

(2020) Acta Crystallogr F Struct Biol Commun 76: 216-221

Released	2016-04-06
Method	X-RAY DIFFRACTION 3.05 Å
Organisms	Homo sapiens
Macromolecule	Multiple coagulation factor deficiency protein 2 (protein) Protein ERGIC-53 (protein)
Unique Ligands	CA, CL