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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Kodera, Y."

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Search Summary

This query matches 11 Structures.

Refinements

Structure Determination Methodology

experimental (11)

Scientific Name of Source Organism

	Corticium sp. (in: basidiomycete fungi) (5)
	Conus magus (1)
	Human immunodeficiency virus 2 (1)
	Human immunodeficiency virus type 2 (ISOLATE GHANA-1) (1)
	Human immunodeficiency virus type 2 subtype A (isolate Ghana-1) (1)
	Stromatopelma calceatum griseipes (1)
	synthetic construct (1)

Taxonomy

	Eukaryota (6)
	Riboviria (2)
	Eukaryota (eukaryotes) (1)
	Riboviria (RNA viruses and viroids) (1)
	other sequences (1)

Experimental Method

	SOLUTION NMR (6)
	X-RAY DIFFRACTION (5)

Polymer Entity Type

Protein (11)

Refinement Resolution (Å)

1.0 - 1.5 (5)

Release Date

	1995 - 1999 (2)
	2000 - 2004 (1)
	2005 - 2009 (3)
	2020 - 2024 (5)

Symmetry Type

	Asymmetric (6)
	Cyclic (5)

SCOP Classification

Small proteins (4)

AllSelected

1 to 11 of 11 Structures

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1LA4 \| pdb_00001la4	Download File View File

Solution Structure of SGTx1

Lee, C.W., Roh, S.H., Kim, S., Endoh, H., Kodera, Y., Maeda, T., Swartz, K.J., Kim, J.I.

(2004) Biochemistry 43: 890-897

Released	2003-11-11
Method	SOLUTION NMR
Organisms	Stromatopelma calceatum griseipes
Macromolecule	SGTx1 (protein)

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1NC8 \| pdb_00001nc8	Download File View File

HIGH-RESOLUTION SOLUTION NMR STRUCTURE OF THE MINIMAL ACTIVE DOMAIN OF THE HUMAN IMMUNODEFICIENCY VIRUS TYPE-2 NUCLEOCAPSID PROTEIN, 15 STRUCTURES

Kodera, Y., Sato, K., Tsukahara, T., Komatsu, H., Maeda, T., Kohno, T.

(1998) Biochemistry 37: 17704-17713

Released	1999-05-25
Method	SOLUTION NMR
Organisms	Human immunodeficiency virus 2
Macromolecule	NUCLEOCAPSID PROTEIN (protein)
Unique Ligands	ZN

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1OMG \| pdb_00001omg	Download File View File

NMR STUDY OF OMEGA-CONOTOXIN MVIIA

Kohno, T., Kim, J.-I., Kobayashi, K., Kodera, Y., Maeda, T., Sato, K.

(1995) Biochemistry 34: 10256-10265

Released	1996-04-03
Method	SOLUTION NMR
Organisms	Conus magus
Macromolecule	OMEGA-CONOTOXIN MVIIA (protein)

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2DI2 \| pdb_00002di2	Download File View File

NMR structure of the HIV-2 nucleocapsid protein

Matsui, T., Kodera, Y., Endoh, H., Miyauchi, E., Komatsu, H., Sato, K., Tanaka, T., Kohno, T., Maeda, T.

(2007) J Biochem 141: 269-277

Released	2007-03-13
Method	SOLUTION NMR
Organisms	synthetic construct
Macromolecule	Nucleocapsid protein p7 (protein)
Unique Ligands	ZN

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2E1X \| pdb_00002e1x	Download File View File

NMR structure of the HIV-2 nucleocapsid protein

Matsui, T., Kodera, Y., Miyauchi, E., Tanaka, H., Endoh, H., Komatsu, H., Tanaka, T., Kohno, T., Maeda, T.

(2007) Biochem Biophys Res Commun 358: 673-678

Released	2007-06-05
Method	SOLUTION NMR
Organisms	Human immunodeficiency virus type 2 subtype A (isolate Ghana-1)
Macromolecule	Gag-Pol polyprotein (Pr160Gag-Pol) (protein)
Unique Ligands	ZN

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2EC7 \| pdb_00002ec7	Download File View File

Solution Structure of Human Immunodificiency Virus Type-2 Nucleocapsid Protein

Matsui, T., Kodera, Y., Tanaka, T., Endoh, H., Tanaka, H., Miyauchi, E., Komatsu, H., Kohno, T., Maeda, T.

(2009) Biochemistry 48: 4314-4323

Released	2008-02-19
Method	SOLUTION NMR
Organisms	Human immunodeficiency virus type 2 (ISOLATE GHANA-1)
Macromolecule	Gag polyprotein (Pr55Gag) (protein)
Unique Ligands	ZN

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7F91 \| pdb_00007f91	Download File View File

SeMet derivative of Thrombocorticin

Kageyama, H., Onodera, K., Sakai, R., Tanaka, Y.

(2022) Nat Commun 13: 7262-7262

Released	2022-07-06
Method	X-RAY DIFFRACTION 1.401 Å
Organisms	Corticium sp. (in: basidiomycete fungi)
Macromolecule	Thrombocorticin (protein)

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7F9F \| pdb_00007f9f	Download File View File

Thrombocorticin

Kageyama, H., Onodera, K., Sakai, R., Tanaka, Y., Freymann, D.M.

(2022) Nat Commun 13: 7262-7262

Released	2022-07-06
Method	X-RAY DIFFRACTION 1.411 Å
Organisms	Corticium sp. (in: basidiomycete fungi)
Macromolecule	Thrombocorticin (protein)
Unique Ligands	MG

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7F9G \| pdb_00007f9g	Download File View File

Thrombocorticin in complex with Ca2+ and fucose

Kageyama, H., Onodera, K., Sakai, R., Tanaka, Y.

(2022) Nat Commun 13: 7262-7262

Released	2022-07-06
Method	X-RAY DIFFRACTION 1.331 Å
Organisms	Corticium sp. (in: basidiomycete fungi)
Macromolecule	Thrombocorticin (protein)
Unique Ligands	CA, FUC

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7F9J \| pdb_00007f9j	Download File View File

Thrombocorticin Q25K in complex with Ca2+

Kageyama, H., Onodera, K., Sakai, R., Tanaka, Y.

(2022) Nat Commun 13: 7262-7262

Released	2022-07-06
Method	X-RAY DIFFRACTION 1.1 Å
Organisms	Corticium sp. (in: basidiomycete fungi)
Macromolecule	Thrombocorticin Q25K mutant (protein)
Unique Ligands	CA

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7FBL \| pdb_00007fbl	Download File View File

Thrombocorticin in complex with Ca2+ and mannose

Kageyama, H., Onodera, K., Sakai, R., Tanaka, Y.

(2022) Nat Commun 13: 7262-7262

Released	2022-07-13
Method	X-RAY DIFFRACTION 1.419 Å
Organisms	Corticium sp. (in: basidiomycete fungi)
Macromolecule	Thrombocorticin (protein)
Unique Ligands	CA, MAN

1 to 11 of 11 Structures

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

1LA4 | pdb_00001la4

Solution Structure of SGTx1

1NC8 | pdb_00001nc8

HIGH-RESOLUTION SOLUTION NMR STRUCTURE OF THE MINIMAL ACTIVE DOMAIN OF THE HUMAN IMMUNODEFICIENCY VIRUS TYPE-2 NUCLEOCAPSID PROTEIN, 15 STRUCTURES

1OMG | pdb_00001omg

NMR STUDY OF OMEGA-CONOTOXIN MVIIA

2DI2 | pdb_00002di2

NMR structure of the HIV-2 nucleocapsid protein

2E1X | pdb_00002e1x

NMR structure of the HIV-2 nucleocapsid protein

2EC7 | pdb_00002ec7

Solution Structure of Human Immunodificiency Virus Type-2 Nucleocapsid Protein

7F91 | pdb_00007f91

SeMet derivative of Thrombocorticin

7F9F | pdb_00007f9f

Thrombocorticin

7F9G | pdb_00007f9g

Thrombocorticin in complex with Ca2+ and fucose

7F9J | pdb_00007f9j

Thrombocorticin Q25K in complex with Ca2+

7FBL | pdb_00007fbl

Thrombocorticin in complex with Ca2+ and mannose

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Symmetry Type

SCOP Classification

1LA4 | pdb_00001la4

1NC8 | pdb_00001nc8

1OMG | pdb_00001omg

2DI2 | pdb_00002di2

2E1X | pdb_00002e1x

2EC7 | pdb_00002ec7

7F91 | pdb_00007f91

7F9F | pdb_00007f9f

7F9G | pdb_00007f9g

7F9J | pdb_00007f9j

7FBL | pdb_00007fbl