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235,183 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Shimada, I."

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Search Summary

This query matches 46 Structures.

Refinements

Structure Determination Methodology

experimental (46)

Scientific Name of Source Organism

	Homo sapiens (27)
	Mus musculus (6)
	Saccharomyces cerevisiae S288C (4)
	Agelenopsis aperta (2)
	Encephalomyocarditis virus (2)
	Escherichia coli (2)
	Grammostola rosea (2)
	Macaca mulatta (2)
	Staphylococcus aureus (2)
	Sus scrofa (2)

More...

Taxonomy

	Eukaryota (41)
	Bacteria (5)
	Eukaryota (eukaryotes) (2)
	Riboviria (2)
	other sequences (2)

Experimental Method

	SOLUTION NMR (23)
	X-RAY DIFFRACTION (17)
	ELECTRON MICROSCOPY (6)

Polymer Entity Type

	Protein (46)
	RNA (2)

Refinement Resolution (Å)

	1.0 - 1.5 (1)
	1.5 - 2.0 (3)
	2.0 - 2.5 (2)
	2.5 - 3.0 (12)
	3.0 - 3.5 (1)
	3.5 - 4.0 (4)

Release Date

	1995 - 1999 (6)
	2000 - 2004 (4)
	2005 - 2009 (4)
	2010 - 2014 (7)
	2015 - 2019 (14)
	2020 - 2024 (11)

Enzyme Classification Name

	Transferases (14)
	Hydrolases (8)

Membrane Protein Annotation

	PDBTM (3)
	OPM (5)
	MemProtMD (2)
	mpstruc (1)

Symmetry Type

	Asymmetric (33)
	Cyclic (13)

SCOP Classification

	Alpha and beta proteins (a+b) (14)
	All beta proteins (5)
	Small proteins (6)
	All alpha proteins (5)
	Alpha and beta proteins (a/b) (2)
	Artifacts (1)
	Membrane and cell surface proteins and peptides (1)

AllSelected

1 to 25 of 46 Structures

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1BDC \| pdb_00001bdc	Download File View File

STAPHYLOCOCCUS AUREUS PROTEIN A, IMMUNOGLOBULIN-BINDING B DOMAIN, NMR, 10 STRUCTURES

Gouda, H., Torigoe, H., Saito, A., Sato, M., Arata, Y., Shimada, I.

(1992) Biochemistry 31: 9665-9672

Released	1997-01-11
Method	SOLUTION NMR
Organisms	Staphylococcus aureus
Macromolecule	STAPHYLOCOCCUS AUREUS PROTEIN A (protein)

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1BDD \| pdb_00001bdd	Download File View File

STAPHYLOCOCCUS AUREUS PROTEIN A, IMMUNOGLOBULIN-BINDING B DOMAIN, NMR, MINIMIZED AVERAGE STRUCTURE

Gouda, H., Torigoe, H., Saito, A., Sato, M., Arata, Y., Shimada, I.

(1992) Biochemistry 31: 9665-9672

Released	1997-01-11
Method	SOLUTION NMR
Organisms	Staphylococcus aureus
Macromolecule	STAPHYLOCOCCUS AUREUS PROTEIN A (protein)

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1D1H \| pdb_00001d1h	Download File View File

SOLUTION STRUCTURE OF HANATOXIN 1

Takahashi, H., Kim, J.I., Sato, K., Swartz, K.J., Shimada, I.

(2000) J Mol Biology 297: 771-780

Released	2000-09-20
Method	SOLUTION NMR
Organisms	Grammostola rosea
Macromolecule	HANATOXIN TYPE 1 (protein)

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1DLF \| pdb_00001dlf	Download File View File

HIGH RESOLUTION CRYSTAL STRUCTURE OF THE FV FRAGMENT FROM AN ANTI-DANSYL SWITCH VARIANT ANTIBODY IGG2A(S) CRYSTALLIZED AT PH 5.25

Nakasako, M., Takahashi, H., Shimada, I., Arata, Y.

(1999) J Mol Biology 291: 117-134

Released	1999-07-26
Method	X-RAY DIFFRACTION 1.45 Å
Organisms	Mus musculus
Macromolecule	ANTI-DANSYL IMMUNOGLOBULIN IGG2A(S) (protein)
Unique Ligands	SO4

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1IE6 \| pdb_00001ie6	Download File View File

SOLUTION STRUCTURE OF IMPERATOXIN A

Lee, C.W., Takeuchi, K., Takahashi, H., Sato, K., Shimada, I., Kim, D.H., Kim, J.I.

(2004) Biochem J 377: 385-394

Released	2003-06-10
Method	SOLUTION NMR
Organisms	Pandinus imperator
Macromolecule	IMPERATOXIN A (protein)

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1KOZ \| pdb_00001koz	Download File View File

SOLUTION STRUCTURE OF OMEGA-GRAMMOTOXIN SIA

Takeuchi, K., Park, E.J., Lee, C.W., Kim, J.I., Takahashi, H., Swartz, K.J., Shimada, I.

(2002) J Mol Biology 321: 517-526

Released	2002-08-28
Method	SOLUTION NMR
Organisms	Grammostola rosea
Macromolecule	Voltage-dependent Channel Inhibitor (protein)

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1L4V \| pdb_00001l4v	Download File View File

SOLUTION STRUCTURE OF SAPECIN

Hanzawa, H., Iwai, H., Takeuchi, K., Kuzuhara, T., Komano, H., Kohda, D., Inagaki, F., Natori, S., Arata, Y., Shimada, I.

(1990) FEBS Lett 269: 413-420

Released	2002-03-27
Method	SOLUTION NMR
Organisms	Sarcophaga peregrina
Macromolecule	Sapecin (protein)

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1OAV \| pdb_00001oav	Download File View File

OMEGA-AGATOXIN IVA

Kim, J.I., Konishi, S., Iwai, H., Kohno, T., Gouda, H., Shimada, I., Sato, K., Arata, Y.

(1995) J Mol Biology 250: 659-671

Released	1995-10-15
Method	SOLUTION NMR
Organisms	Agelenopsis aperta
Macromolecule	OMEGA-AGATOXIN IVA (protein)

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1OAW \| pdb_00001oaw	Download File View File

OMEGA-AGATOXIN IVA

Kim, J.I., Konishi, S., Iwai, H., Kohno, T., Gouda, H., Shimada, I., Sato, K., Arata, Y.

(1995) J Mol Biology 250: 659-671

Released	1995-10-15
Method	SOLUTION NMR
Organisms	Agelenopsis aperta
Macromolecule	OMEGA-AGATOXIN IVA (protein)

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1WZ1 \| pdb_00001wz1	Download File View File

Crystal structure of the Fv fragment complexed with dansyl-lysine

Nakasako, M., Oka, T., Mashumo, M., Takahashi, H., Shimada, I., Yamaguchi, Y., Kato, K., Arata, Y.

(2005) J Mol Biology 351: 627-640

Released	2006-01-31
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Mus musculus
Macromolecule	Ig heavy chain (protein) Ig light chain (protein)
Unique Ligands	DNS

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2DLF \| pdb_00002dlf	Download File View File

HIGH RESOLUTION CRYSTAL STRUCTURE OF THE FV FRAGMENT FROM AN ANTI-DANSYL SWITCH VARIANT ANTIBODY IGG2A(S) CRYSTALLIZED AT PH 6.75

Nakasako, M., Takahashi, H., Shimada, I., Arata, Y.

(1999) J Mol Biology 291: 117-134

Released	1999-12-17
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Mus musculus
Macromolecule	PROTEIN (ANTI-DANSYL IMMUNOGLOBULIN IGG2A(S) (HEAVY CHAIN)) (protein) PROTEIN (ANTI-DANSYL IMMUNOGLOBULIN IGG2A(S)-KAPPA (LIGHT CHAIN)) (protein)
Unique Ligands	SO4

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2I83 \| pdb_00002i83	Download File View File

hyaluronan-binding domain of CD44 in its ligand-bound form

Takeda, M., Ogino, S., Umemoto, R., Sakakura, M., Kajiwara, M., Sugahara, K.N., Hayasaka, H., Miyasaka, M., Terasawa, H., Shimada, I.

(2006) J Biological Chem 281: 40089-40095

Released	2006-11-21
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	CD44 antigen (protein)

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2LMK \| pdb_00002lmk	Download File View File

Solution Structure of Mouse Pheromone ESP1

Yoshinaga, S., Sato, T., Hirakane, M., Esaki, K., Hamaguchi, T., Haga-Yamanaka, S., Tsunoda, M., Kimoto, H., Shimada, I., Touhara, K., Terasawa, H.

(2013) J Biological Chem

Released	2013-04-17
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	Exocrine gland-secreting peptide 1 (protein)

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2MLO \| pdb_00002mlo	Download File View File

Human CCR2 Membrane-Proximal C-Terminal Region (PRO-C) in a Membrane bound form

Esaki, K., Yoshinaga, S., Tsuji, T., Toda, E., Terashima, Y., Saitoh, T., Kohda, D., Kohno, T., Osawa, M., Ueda, T., Shimada, I., Matsushima, K., Terasawa, H.

(2014) FEBS J 281: 5552-5566

Released	2014-10-08
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	MCP-1 receptor (protein)

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2MLQ \| pdb_00002mlq	Download File View File

Human CCR2 Membrane-Proximal C-Terminal Region (PRO-C) in a frount bound form

Esaki, K., Yoshinaga, S., Tsuji, T., Toda, E., Terashima, Y., Saitoh, T., Kohda, D., Kohno, T., Osawa, M., Ueda, T., Shimada, I., Matsushima, K., Terasawa, H.

(2014) FEBS J 281: 5552-5566

Released	2014-10-08
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	MCP-1 receptor (protein)

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2NOO \| pdb_00002noo	Download File View File

Crystal Structure of Mutant NikA

Addy, C., Ohara, M., Kawai, F., Kidera, A., Ikeguchi, M., Fuchigami, S., Osawa, M., Shimada, I., Park, S.Y., Tame, J.R.H., Heddle, J.G.

(2007) Acta Crystallogr D Biol Crystallogr 63: 221-229

Released	2007-01-23
Method	X-RAY DIFFRACTION 1.65 Å
Organisms	Escherichia coli K-12
Macromolecule	Nickel-binding periplasmic protein (protein)
Unique Ligands	IOD, NI

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2RQG \| pdb_00002rqg	Download File View File

Structure of GSPT1/ERF3A-PABC

Osawa, M., Nakanishi, T., Hosoda, N., Uchida, S., Hoshino, T., Katada, I., Shimada, I.

To be published

Released	2010-05-26
Method	SOLUTION NMR
Organisms	Homo sapiens Mus musculus
Macromolecule	G1 to S phase transition 1 (protein) Polyadenylate-binding protein 1 (protein)

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2RQH \| pdb_00002rqh	Download File View File

Structure of GSPT1/ERF3A-PABC

Osawa, M., Nakanishi, T., Hosoda, N., Uchida, S., Hoshino, T., Katada, I., Shimada, I.

To be published

Released	2010-05-26
Method	SOLUTION NMR
Organisms	Homo sapiens Mus musculus
Macromolecule	G1 to S phase transition 1 (protein) Polyadenylate-binding protein 1 (protein)

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2RR8 \| pdb_00002rr8	Download File View File

Solution structure of calponin homology domain of IQGAP1

Umemoto, R., Nishida, N., Ogino, S., Shimada, I.

(2010) J Biomol NMR 48: 59-64

Released	2010-09-15
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	IQGAP1 protein (protein)

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2RSG \| pdb_00002rsg	Download File View File

Solution structure of the CERT PH domain

Sugiki, T., Takeuchi, K., Tokunaga, Y., Kumagai, K., Kawano, M., Nishijima, M., Hanada, K., Takahashi, H., Shimada, I.

(2012) J Biological Chem 287: 33706-33718

Released	2012-08-15
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Collagen type IV alpha-3-binding protein (protein)

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2Z4F \| pdb_00002z4f	Download File View File

Solution structure of the Discoidin Domain of DDR2

Ichikawa, O., Osawa, M., Nishida, N., Goshima, N., Nomura, N., Shimada, I.

(2007) EMBO J 26: 4168-4176

Released	2007-09-04
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Discoidin domain-containing receptor 2 (protein)

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3WZZ \| pdb_00003wzz	Download File View File

Crystal structure of PIP4KIIBETA

Takeuchi, K., Lo, Y.H., Sumita, K., Senda, M., Terakawa, J., Dimitoris, A., Locasale, J.W., Sasaki, M., Yoshino, H., Zhang, Y., Kahoud, E.R., Takano, T., Yokota, T., Emerling, B., Asara, J.A., Ishida, T., Shimada, I., Daikoku, T., Cantley, L.C., Senda, T., Sasaki, A.T.

(2016) Mol Cell 61: 187-198

Released	2015-10-14
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Homo sapiens
Macromolecule	Phosphatidylinositol 5-phosphate 4-kinase type-2 beta (protein)

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3X01 \| pdb_00003x01	Download File View File

Crystal structure of PIP4KIIBETA complex with AMP

(2016) Mol Cell 61: 187-198

Released	2015-10-14
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Homo sapiens
Macromolecule	Phosphatidylinositol 5-phosphate 4-kinase type-2 beta (protein)
Unique Ligands	AMP

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3X02 \| pdb_00003x02	Download File View File

Crystal structure of PIP4KIIBETA complex with GMP

(2016) Mol Cell 61: 187-198

Released	2015-10-14
Method	X-RAY DIFFRACTION 2.45 Å
Organisms	Homo sapiens
Macromolecule	Phosphatidylinositol 5-phosphate 4-kinase type-2 beta (protein)
Unique Ligands	5GP

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3X03 \| pdb_00003x03	Download File View File

Crystal structure of PIP4KIIBETA complex with AMPPNP

(2016) Mol Cell 61: 187-198

Released	2015-10-14
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Homo sapiens
Macromolecule	Phosphatidylinositol 5-phosphate 4-kinase type-2 beta (protein)
Unique Ligands	ANP

1 to 25 of 46 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

1BDC | pdb_00001bdc

1BDD | pdb_00001bdd

1D1H | pdb_00001d1h

1DLF | pdb_00001dlf

1IE6 | pdb_00001ie6

1KOZ | pdb_00001koz

1L4V | pdb_00001l4v

1OAV | pdb_00001oav

1OAW | pdb_00001oaw

1WZ1 | pdb_00001wz1

2DLF | pdb_00002dlf

2I83 | pdb_00002i83

2LMK | pdb_00002lmk

2MLO | pdb_00002mlo

2MLQ | pdb_00002mlq

2NOO | pdb_00002noo

2RQG | pdb_00002rqg

2RQH | pdb_00002rqh

2RR8 | pdb_00002rr8

2RSG | pdb_00002rsg

2Z4F | pdb_00002z4f

3WZZ | pdb_00003wzz

3X01 | pdb_00003x01

3X02 | pdb_00003x02

3X03 | pdb_00003x03