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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Citation Author = "Matsui, T."

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Search Summary

This query matches 24 Structures.

Refinements

Structure Determination Methodology

experimental (24)

Scientific Name of Source Organism

	Homo sapiens (14)
	Human adenovirus D8 (5)
	Human adenovirus 2 (2)
	Mus musculus (2)
	synthetic construct (2)
	Staphylococcus aureus (1)

Taxonomy

	Eukaryota (16)
	Varidnaviria (7)
	other sequences (2)
	Bacteria (1)

Experimental Method

X-RAY DIFFRACTION (24)

Polymer Entity Type

	Protein (24)
	DNA (1)

Refinement Resolution (Å)

	1.0 - 1.5 (5)
	1.5 - 2.0 (7)
	2.0 - 2.5 (6)
	2.5 - 3.0 (4)
	3.0 - 3.5 (2)

Release Date

	2010 - 2014 (7)
	2015 - 2019 (13)
	2020 - 2024 (4)

Enzyme Classification Name

	Hydrolases (23)
	Isomerases (1)

Symmetry Type

	Asymmetric (20)
	Cyclic (4)

SCOP Classification

	All beta proteins (5)
	Artifacts (1)

AllSelected

1 to 24 of 24 Structures

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3V4L \| pdb_00003v4l	Download File View File

Mouse MALT1(caspase-IG3 domains) in complex with a irreversible peptidic inhibitor

Renatus, M., Wiesmann, C.

(2012) J Mol Biology 419: 4-21

Released	2012-03-14
Method	X-RAY DIFFRACTION 3.15 Å
Organisms	Mus musculus
Macromolecule	MALT1 Inhibitor (protein) Mucosa-associated lymphoid tissue lymphoma translocation protein 1 homolog (protein)

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3V4O \| pdb_00003v4o	Download File View File

Human MALT1 (caspase domain) in complex with an irreversible peptidic inhibitor

Renatus, M., Wiesmann, C.

(2012) J Mol Biology 419: 4-21

Released	2012-03-14
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	MALT1 Inhibitor (protein) Mucosa-associated lymphoid tissue lymphoma translocation protein 1 (protein)

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3V55 \| pdb_00003v55	Download File View File

Human MALT1 (334-719) in its ligand free form

Renatus, M., Wiesmann, C.

(2012) J Mol Biology 419: 4-21

Released	2012-03-14
Method	X-RAY DIFFRACTION 1.81 Å
Organisms	Homo sapiens
Macromolecule	Mucosa-associated lymphoid tissue lymphoma translocation protein 1 (protein)

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4PID \| pdb_00004pid	Download File View File

Crystal structure of human adenovirus 2 protease with a weak pyrimidine nitrile inhibitor

Mac Sweeney, A., Grosche, P., Ellis, D., Combrink, K., Erbel, P., Hughes, N., Sirockin, F., Melkko, S., Bernardi, A., Ramage, P., Jarousse, N., Altmann, E.

(2014) ACS Med Chem Lett 5: 937-941

Released	2014-09-10
Method	X-RAY DIFFRACTION 1.59 Å
Organisms	Human adenovirus 2
Macromolecule	Pre-protein VI (protein) Protease (protein)
Unique Ligands	2UQ, ACT

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4PIE \| pdb_00004pie	Download File View File

Crystal structure of human adenovirus 2 protease a substrate based nitrile inhibitor

Mac Sweeney, A., Grosche, P., Ellis, D., Combrink, C., Erbel, C., Hughes, N., Sirockin, F., Melkko, S., Bernardi, A., Ramage, P., Jarousse, N., Altmann, E.

(2014) ACS Med Chem Lett 5: 937-941

Released	2014-09-10
Method	X-RAY DIFFRACTION 1.94 Å
Organisms	Human adenovirus 2
Macromolecule	Pre-protein VI (protein) Protease (protein)
Unique Ligands	3FO, ACT, SO4, ZN

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4PIQ \| pdb_00004piq	Download File View File

Crystal structure of human adenovirus 8 protease with a nitrile inhibitor

Mac Sweeney, A., Grosche, P., Ellis, D., Combrink, K., Erbel, P., Hughes, N., Sirockin, F., Melkko, S., Bernardi, A., Ramage, P., Jarousse, N., Altmann, E.

(2014) ACS Med Chem Lett 5: 937-941

Released	2014-09-10
Method	X-RAY DIFFRACTION 2.07 Å
Organisms	Human adenovirus D8
Macromolecule	PVI (protein) Protease (protein)
Unique Ligands	3FS

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4PIS \| pdb_00004pis	Download File View File

Crystal structure of human adenovirus 8 protease in complex with a nitrile inhibitor

Mac Sweeney, A., Grosche, P., Ellis, D., Combrink, K., Erbel, P., Hughes, N., Sirockin, F., Melkko, S., Bernardi, A., Ramage, P., Jarousse, N., Altmann, E.

(2014) ACS Med Chem Lett 5: 937-941

Released	2014-09-10
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Human adenovirus D8
Macromolecule	PVI (protein) Protease (protein)
Unique Ligands	3FU

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4WX4 \| pdb_00004wx4	Download File View File

Crystal structure of adenovirus 8 protease in complex with a nitrile inhibitor

Grosche, P., Sirockin, F., Mac Sweeney, A., Ramage, P., Erbel, P., Melkko, S., Bernardi, A., Hughes, N., Ellis, D., Combrink, K., Jarousse, N., Altmann, E.

(2015) Bioorg Med Chem Lett 25: 438-443

Released	2015-01-14
Method	X-RAY DIFFRACTION 1.03 Å
Organisms	Human adenovirus D8 synthetic construct
Macromolecule	Protease (protein) peptide (protein)
Unique Ligands	3VF, EPE, GLY

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4WX6 \| pdb_00004wx6	Download File View File

Crystal structure of human adenovirus 8 protease with an irreversible vinyl sulfone inhibitor

Grosche, P., Sirockin, F., Mac Sweeney, A., Ramage, P., Erbel, P., Melkko, S., Bernardi, A., Hughes, N., Ellis, D., Combrink, K., Jarousse, N., Altmann, E.

(2015) Bioorg Med Chem Lett 25: 438-443

Released	2015-01-14
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Human adenovirus D8
Macromolecule	PVI (protein) Protease (protein)
Unique Ligands	3VK

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4WX7 \| pdb_00004wx7	Download File View File

Crystal structure of adenovirus 8 protease with a nitrile inhibitor

Grosche, P., Sirockin, F., Mac Sweeney, A., Ramage, P., Erbel, P., Melkko, S., Bernardi, A., Hughes, N., Ellis, D., Combrink, K., Jarousse, N., Altmann, E.

(2015) Bioorg Med Chem Lett 25: 438-443

Released	2015-01-14
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Human adenovirus D8
Macromolecule	PVI (protein) Protease (protein)
Unique Ligands	3VJ

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5FAH \| pdb_00005fah	Download File View File

KALLIKREIN-7 IN COMPLEX WITH COMPOUND1

Ostermann, N., Zink, F.

(2016) Nat Chem Biol 12: 1105-1110

Released	2016-10-26
Method	X-RAY DIFFRACTION 1.1 Å
Organisms	Homo sapiens
Macromolecule	Kallikrein-7 (protein)
Unique Ligands	5VT, ACT

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5FBE \| pdb_00005fbe	Download File View File

COMPLEMENT FACTOR D IN COMPLEX WITH COMPOUND2

Ostermann, N., Zink, F.

(2016) Nat Chem Biol 12: 1105-1110

Released	2016-10-26
Method	X-RAY DIFFRACTION 1.43 Å
Organisms	Homo sapiens
Macromolecule	Complement factor D (protein)
Unique Ligands	5W5, GOL

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5FBI \| pdb_00005fbi	Download File View File

COMPLEMENT FACTOR D IN COMPLEX WITH COMPOUND 3b

Ostermann, N., Zink, F.

(2016) Nat Chem Biol 12: 1105-1110

Released	2016-10-26
Method	X-RAY DIFFRACTION 1.47 Å
Organisms	Homo sapiens
Macromolecule	Complement factor D (protein)
Unique Ligands	5WD, GOL

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5FCK \| pdb_00005fck	Download File View File

COMPLEMENT FACTOR D IN COMPLEX WITH COMPOUND 5

Mac Sweeney, A.

(2016) Nat Chem Biol 12: 1105-1110

Released	2016-10-26
Method	X-RAY DIFFRACTION 1.86 Å
Organisms	Homo sapiens
Macromolecule	Complement factor D (protein)
Unique Ligands	5WC, SO4

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5FCR \| pdb_00005fcr	Download File View File

MOUSE COMPLEMENT FACTOR D

Mac Sweeney, A.

(2016) Nat Chem Biol 12: 1105-1110

Released	2016-10-26
Method	X-RAY DIFFRACTION 1.25 Å
Organisms	Mus musculus
Macromolecule	Complement factor D (protein)
Unique Ligands	DMS, EPE, GOL, SO4

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6F7I \| pdb_00006f7i	Download File View File

human MALT1(329-728) IN COMPLEX WITH MLT-747

Renatus, M., Renatus, M.

(2019) Nat Chem Biol 15: 304-313

Released	2019-01-02
Method	X-RAY DIFFRACTION 2.43 Å
Organisms	Homo sapiens
Macromolecule	Mucosa-associated lymphoid tissue lymphoma translocation protein 1 (protein)
Unique Ligands	CW5, GOL, MG

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6H4A \| pdb_00006h4a	Download File View File

Human MALT1(329-728) in complex with MLT-748

Renatus, M., Renatus, M.

(2019) Nat Chem Biol 15: 304-313

Released	2019-02-13
Method	X-RAY DIFFRACTION 2.65 Å
Organisms	Homo sapiens
Macromolecule	Mucosa-associated lymphoid tissue lymphoma translocation protein 1 (protein)
Unique Ligands	FNB

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6QSW \| pdb_00006qsw	Download File View File

Complement factor B protease domain in complex with the reversible inhibitor N-(2-bromo-4-methylnaphthalen-1-yl)-4,5-dihydro-1H-imidazol-2-amine.

Adams, C.M., Sellner, H., Ehara, T., Mac Sweeney, A., Crowley, M., Anderson, K., Karki, R., Mainolfi, N., Valeur, E., Sirockin, F., Gerhartz, B., Erbel, P., Hughes, N., Smith, T.M., Cumin, F., Argikar, U., Mogi, M., Sedrani, R., Wiesmann, C., Jaffee, B., Maibaum, J., Flohr, S., Harrison, R., Eder, J.

(2019) Proc Natl Acad Sci U S A 116: 7926-7931

Released	2019-03-27
Method	X-RAY DIFFRACTION 1.64 Å
Organisms	Homo sapiens
Macromolecule	Complement factor B (protein)
Unique Ligands	JGT, SO4

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6QSX \| pdb_00006qsx	Download File View File

Complement factor B protease domain in complex with the reversible inhibitor ((2S,4S)-1-((5,7-dimethyl-1H-indol-4-yl)methyl)-4-methoxypiperidin-2-yl)methanol.

(2019) Proc Natl Acad Sci U S A 116: 7926-7931

Released	2019-03-27
Method	X-RAY DIFFRACTION 1.77 Å
Organisms	Homo sapiens
Macromolecule	Complement factor B (protein)
Unique Ligands	JGN, SO4, ZN

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6RAV \| pdb_00006rav	Download File View File

Complement factor B protease domain in complex with the reversible inhibitor 4-((2S,4S)-4-ethoxy-1-((5-methoxy-7-methyl-1H-indol-4-yl)methyl)piperidin-2-yl)benzoic acid

(2019) Proc Natl Acad Sci U S A 116: 7926-7931

Released	2019-04-17
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Homo sapiens
Macromolecule	Complement factor B (protein)
Unique Ligands	JGQ, SO4, ZN

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6YN8 \| pdb_00006yn8	Download File View File

Human MALT1(334-719) in complex with a tetrazole containing compound

Renatus, M.

(2020) Adv Ther (Weinh) 3:

Released	2020-06-24
Method	X-RAY DIFFRACTION 3.052 Å
Organisms	Homo sapiens
Macromolecule	Mucosa-associated lymphoid tissue lymphoma translocation protein 1 (protein)
Unique Ligands	OZK

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6YN9 \| pdb_00006yn9	Download File View File

MALT1(329-728) in complex with a sulfonamide containing compound

Renatus, M.

(2020) Adv Ther (Weinh) 3:

Released	2020-06-24
Method	X-RAY DIFFRACTION 2.558 Å
Organisms	Homo sapiens
Macromolecule	Mucosa-associated lymphoid tissue lymphoma translocation protein 1 (protein)
Unique Ligands	OZQ

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7ALV \| pdb_00007alv	Download File View File

Crystal Structure of NLRP3 NACHT domain in complex with a potent inhibitor

Dekker, C., Hinniger, A.

(2021) J Mol Biology 433: 167309-167309

Released	2021-10-20
Method	X-RAY DIFFRACTION 2.835 Å
Organisms	Homo sapiens
Macromolecule	NACHT, LRR and PYD domains-containing protein 3 (protein)
Unique Ligands	ADP, RM5

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8BP2 \| pdb_00008bp2	Download File View File

2.8A STRUCTURE OF ZOLIFLODACIN WITH S.AUREUS DNA GYRASE AND DNA

Bax, B.D., Morgan, H., Warren, A.J.

(2023) Int J Mol Sci 24:

Released	2023-02-08
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Staphylococcus aureus synthetic construct
Macromolecule	DNA gyrase subunit A (protein) DNA gyrase subunit B (protein) DNA (20-MER) (nucleic acid)
Unique Ligands	BTB, GOL, MN, NA, R8U

1 to 24 of 24 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

Symmetry Type

SCOP Classification

3V4L | pdb_00003v4l

3V4O | pdb_00003v4o

3V55 | pdb_00003v55

4PID | pdb_00004pid

4PIE | pdb_00004pie

4PIQ | pdb_00004piq

4PIS | pdb_00004pis

4WX4 | pdb_00004wx4

4WX6 | pdb_00004wx6

4WX7 | pdb_00004wx7

5FAH | pdb_00005fah

5FBE | pdb_00005fbe

5FBI | pdb_00005fbi

5FCK | pdb_00005fck

5FCR | pdb_00005fcr

6F7I | pdb_00006f7i

6H4A | pdb_00006h4a

6QSW | pdb_00006qsw

6QSX | pdb_00006qsx

6RAV | pdb_00006rav

6YN8 | pdb_00006yn8

6YN9 | pdb_00006yn9

7ALV | pdb_00007alv

8BP2 | pdb_00008bp2