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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Imai, Y."

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Search Summary

This query matches 9 Structures.

Refinements

Structure Determination Methodology

experimental (9)

Scientific Name of Source Organism

	Homo sapiens (4)
	synthetic construct (4)
	Escherichia coli O157:H7 (2)
	Escherichia coli K-12 (1)
	Mus musculus (1)
	Mycobacterium tuberculosis H37Rv (1)
	Photorhabdus noenieputensis (1)

Taxonomy

	Eukaryota (5)
	Bacteria (4)
	other sequences (4)

Experimental Method

	X-RAY DIFFRACTION (8)
	ELECTRON MICROSCOPY (1)

Polymer Entity Type

	Protein (9)
	DNA (1)

Refinement Resolution (Å)

	2.0 - 2.5 (5)
	2.5 - 3.0 (2)
	3.0 - 3.5 (2)

Release Date

	2005 - 2009 (2)
	2020 - 2024 (7)

Enzyme Classification Name

	Hydrolases (3)
	Isomerases (1)
	Ligases (1)
	Transferases (1)

Membrane Protein Annotation

	MemProtMD (3)
	OPM (3)
	PDBTM (3)
	mpstruc (3)

Symmetry Type

	Asymmetric (9)
	Cyclic (1)

SCOP Classification

	Alpha and beta proteins (a+b) (1)
	Artifacts (1)

AllSelected

1 to 9 of 9 Structures

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1WY9 \| pdb_00001wy9	Download File View File

Crystal structure of microglia-specific protein, Iba1

Yamada, M., Imai, Y., Kohsaka, S., Kamitori, S.

(2006) J Mol Biology 364: 449-457

Released	2006-02-21
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Mus musculus
Macromolecule	Allograft inflammatory factor 1 (protein)
Unique Ligands	CA

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2CYX \| pdb_00002cyx	Download File View File

Structure of human ubiquitin-conjugating enzyme E2 G2 (UBE2G2/UBC7)

Yoshikawa, S., Arai, R., Murayama, K., Imai, Y., Takahashi, R., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2006) Acta Crystallogr Sect F Struct Biol Cryst Commun 62: 330-334

Released	2006-04-25
Method	X-RAY DIFFRACTION 2.56 Å
Organisms	Homo sapiens
Macromolecule	Ubiquitin-conjugating enzyme E2 G2 (protein)

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7NRE \| pdb_00007nre	Download File View File

Crystal structure of E.coli BamA beta-barrel in complex with darobactin (crystal form 1)

Jakob, R.P., Kaur, H., Marzinek, J.K., Green, R., Imai, Y., Bolla, J., Robinson, C., Bond, P.J., Lewis, K., Maier, T., Hiller, S.

(2021) Nature 593: 125-129

Released	2021-04-21
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Escherichia coli O157:H7 synthetic construct
Macromolecule	Darobactin (protein) Outer membrane protein assembly factor BamA (protein)
Unique Ligands	C8E, MG

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7NRF \| pdb_00007nrf	Download File View File

Crystal structure of E.coli BamA beta-barrel in complex with darobactin (crystal form 2)

Jakob, R.P., Kaur, H., Marzinek, J.K., Green, R., Imai, Y., Bolla, J., Robinson, C., Bond, P.J., Lewis, K., Maier, T., Hiller, S.

(2021) Nature 593: 125-129

Released	2021-04-21
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Escherichia coli O157:H7 synthetic construct
Macromolecule	Darobactin (protein) Outer membrane protein assembly factor BamA (protein)
Unique Ligands	C8E, MG

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7NRI \| pdb_00007nri	Download File View File

Structure of the darobactin-bound E. coli BAM complex (BamABCDE)

Jakob, R.P., Kaur, H., Marzinek, J.K., Green, R., Imai, Y., Bolla, J., Robinson, C., Bond, P.J., Lewis, K., Maier, T., Hiller, S.

(2021) Nature 593: 125-129

Released	2021-04-21
Method	ELECTRON MICROSCOPY 3.03 Å
Organisms	Escherichia coli K-12 synthetic construct
Macromolecule	Unique protein chains: 6

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7UGW \| pdb_00007ugw	Download File View File

M. tuberculosis DNA gyrase cleavage core bound to DNA and evybactin

Hauk, G., Imai, Y., Lewis, K., Berger, J.M.

(2022) Nat Chem Biol 18: 1236-1244

Released	2022-08-17
Method	X-RAY DIFFRACTION 3 Å
Organisms	Mycobacterium tuberculosis H37Rv Photorhabdus noenieputensis synthetic construct
Macromolecule	DNA gyrase subunit A (protein) DNA gyrase subunit B (protein) evybactin (protein) DNA (46-MER) (nucleic acid)
Unique Ligands	MG

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7YI7 \| pdb_00007yi7	Download File View File

Crystal structure of Human HPSE1 in complex with inhibitor

Mima, M., Fujimoto, N., Imai, Y.

(2022) Bioorg Med Chem Lett 79: 129050-129050

Released	2022-12-07
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Homo sapiens
Macromolecule	Heparanase 50 kDa subunit (protein) Heparanase 8 kDa subunit (protein)
Unique Ligands	IUV

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7YJC \| pdb_00007yjc	Download File View File

Crystal structure of Human HPSE1 in complex with inhibitor

Mima, M., Fujimoto, N., Imai, Y.

(2022) Bioorg Med Chem Lett 79: 129050-129050

Released	2022-12-07
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	Heparanase 50 kDa subunit (protein) Heparanase 8 kDa subunit (protein)
Unique Ligands	IVO

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8JYG \| pdb_00008jyg	Download File View File

Crystal structure of Human HPSE1 in complex with inhibitor

Mima, M., Fujimoto, N., Imai, Y.

(2023) Bioorg Med Chem 93: 117460-117460

Released	2023-09-20
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	Heparanase (protein) Heparanase 50 kDa subunit (protein)
Unique Ligands	EDO, NAG, V8R

1 to 9 of 9 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.

1WY9 | pdb_00001wy9

Crystal structure of microglia-specific protein, Iba1

2CYX | pdb_00002cyx

Structure of human ubiquitin-conjugating enzyme E2 G2 (UBE2G2/UBC7)

7NRE | pdb_00007nre

Crystal structure of E.coli BamA beta-barrel in complex with darobactin (crystal form 1)

7NRF | pdb_00007nrf

Crystal structure of E.coli BamA beta-barrel in complex with darobactin (crystal form 2)

7NRI | pdb_00007nri

Structure of the darobactin-bound E. coli BAM complex (BamABCDE)

7UGW | pdb_00007ugw

M. tuberculosis DNA gyrase cleavage core bound to DNA and evybactin

7YI7 | pdb_00007yi7

Crystal structure of Human HPSE1 in complex with inhibitor

7YJC | pdb_00007yjc

Crystal structure of Human HPSE1 in complex with inhibitor

8JYG | pdb_00008jyg

Crystal structure of Human HPSE1 in complex with inhibitor

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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

1WY9 | pdb_00001wy9

2CYX | pdb_00002cyx

7NRE | pdb_00007nre

7NRF | pdb_00007nrf

7NRI | pdb_00007nri

7UGW | pdb_00007ugw

7YI7 | pdb_00007yi7

7YJC | pdb_00007yjc

8JYG | pdb_00008jyg