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234,440 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Yoshizawa, T."

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Search Summary

This query matches 60 Structures.

Refinements

Structure Determination Methodology

experimental (60)

Scientific Name of Source Organism

	Homo sapiens (23)
	Bacillus cereus VD045 (8)
	Chlorobium limicola (6)
	Escherichia coli (5)
	synthetic construct (5)
	Thaumatococcus daniellii (4)
	Bos taurus (3)
	Hepacivirus hominis (3)
	Monkeypox virus (3)
	Chloracidobacterium thermophilum B (2)

More...

Taxonomy

	Eukaryota (36)
	Bacteria (25)
	other sequences (5)
	Riboviria (3)
	Varidnaviria (3)
	Duplodnaviria (1)

Experimental Method

	X-RAY DIFFRACTION (43)
	ELECTRON MICROSCOPY (17)

Polymer Entity Type

	Protein (60)
	DNA (4)
	RNA (2)

Refinement Resolution (Å)

	1.0 - 1.5 (1)
	1.5 - 2.0 (11)
	2.0 - 2.5 (20)
	2.5 - 3.0 (16)
	3.0 - 3.5 (11)
	3.5 - 4.0 (1)

Release Date

	2005 - 2009 (1)
	2010 - 2014 (3)
	2015 - 2019 (14)
	2020 - 2024 (32)
	2025 - 2029 (10)

Enzyme Classification Name

	Hydrolases (14)
	Transferases (5)
	Lyases (2)
	Oxidoreductases (1)

Membrane Protein Annotation

	PDBTM (8)
	MemProtMD (5)
	mpstruc (5)
	OPM (2)

Symmetry Type

	Asymmetric (42)
	Cyclic (11)
	Dihedral (8)

SCOP Classification

	Alpha and beta proteins (a/b) (5)
	Alpha and beta proteins (a+b) (5)
	All beta proteins (4)

AllSelected

1 to 25 of 60 Structures

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3FHR \| pdb_00003fhr	Download File View File

High resolution crystal structure of mitogen-activated protein kinase-activated protein kinase 3 (MK3)-inhibitor complex

Cheng, R.K.Y., Barker, J., Palan, S., Felicetti, B., Whittaker, M., Hesterkamp, T.

(2010) Protein Sci 19: 168-173

Released	2009-12-15
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	MAP kinase-activated protein kinase 3 (protein)
Unique Ligands	P4O

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3RVB \| pdb_00003rvb	Download File View File

The structure of HCV NS3 helicase (Heli-80) bound with inhibitor ITMN-3479

Mather, O., Cheng, R., Schonfield, D., Barker, J.

To be published

Released	2014-09-24
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Hepacivirus hominis
Macromolecule	RNA helicase (protein)
Unique Ligands	CL, I79, MG

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4AUA \| pdb_00004aua	Download File View File

Liganded X-ray crystal structure of cyclin dependent kinase 6 (CDK6)

Cho, Y.S., Angove, H., Brain, C., Chen, C.H.T., Cheng, R., Chopra, R., Chung, K., Congreve, M., Dagostin, C., Davis, D., Feltell, R., Giraldes, J., Hiscock, S., Kim, S., Kovats, S., Lagu, B., Lewry, K., Loo, A., Lu, Y., Luzzio, M., Maniara, W., Mcmenamin, R., Mortenson, P., Benning, R., O'Reilly, M., Rees, D., Shen, J., Smith, T., Wang, Y., Williams, G., Woolford, A., Wrona, W., Xu, M., Yang, F., Howard, S.

(2012) ACS Med Chem Lett 3: 445-449

Released	2013-02-06
Method	X-RAY DIFFRACTION 2.31 Å
Organisms	Homo sapiens
Macromolecule	CYCLIN-DEPENDENT KINASE 6 (protein)
Unique Ligands	4AU

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4EZ5 \| pdb_00004ez5	Download File View File

CDK6 (monomeric) in complex with inhibitor

Chopra, R., Xu, M.

(2012) ACS Med Chem Lett 3: 445-449

Released	2013-02-06
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Homo sapiens
Macromolecule	Cyclin-dependent kinase 6 (protein)
Unique Ligands	0RS

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4WXP \| pdb_00004wxp	Download File View File

X-ray crystal structure of NS3 Helicase from HCV with a bound fragment inhibitor at 2.08 A resolution

Davies, D.R.

To be published

Released	2015-12-23
Method	X-RAY DIFFRACTION 2.08 Å
Organisms	Hepacivirus hominis
Macromolecule	NS3-4 protease (protein)
Unique Ligands	3VY, CL, NA

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4WXR \| pdb_00004wxr	Download File View File

X-ray crystal structure of NS3 Helicase from HCV with a bound inhibitor at 2.42 A resolution

Davies, D.R., Kim, H., Lorimer, D.

To be published

Released	2015-12-23
Method	X-RAY DIFFRACTION 2.42 Å
Organisms	Hepacivirus hominis
Macromolecule	NS3 (protein)
Unique Ligands	3VZ

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5NJM \| pdb_00005njm	Download File View File

Lysozyme room-temperature structure determined by serial millisecond crystallography

Weinert, T., Vera, L., Marsh, M., James, D., Gashi, D., Nogly, P., Jaeger, K., Standfuss, J.

(2017) Nat Commun 8: 542-542

Released	2017-09-27
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Gallus gallus
Macromolecule	Lysozyme C (protein)

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5NLX \| pdb_00005nlx	Download File View File

A2A Adenosine receptor room-temperature structure determined by serial millisecond crystallography

Weinert, T., Cheng, R., James, D., Gashi, D., Nogly, P., Jaeger, K., Dore, A.S., Geng, T., Cooke, R., Hennig, M., Standfuss, J.

(2017) Nat Commun 8: 542-542

Released	2017-09-27
Method	X-RAY DIFFRACTION 2.14 Å
Organisms	Escherichia coli Homo sapiens
Macromolecule	Adenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a (protein)
Unique Ligands	CLR, NA, OLA, ZMA

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5NM2 \| pdb_00005nm2	Download File View File

A2A Adenosine receptor cryo structure

Weinert, T., Cheng, R., James, D., Gashi, D., Nogly, P., Jaeger, K., Dore, A.S., Geng, T., Cooke, R., Hennig, M., Standfuss, J.

(2017) Nat Commun 8: 542-542

Released	2017-09-27
Method	X-RAY DIFFRACTION 1.948 Å
Organisms	Escherichia coli Homo sapiens
Macromolecule	Adenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a (protein)
Unique Ligands	CLR, NA, OLA, OLB, OLC, ZMA

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5NM4 \| pdb_00005nm4	Download File View File

A2A Adenosine receptor room-temperature structure determined by serial femtosecond crystallography

Weinert, T., Cheng, R., James, D., Gashi, D., Nogly, P., Jaeger, K., Hennig, M., Standfuss, J.

(2017) Nat Commun 8: 542-542

Released	2017-09-27
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Escherichia coli Homo sapiens
Macromolecule	Adenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a (protein)
Unique Ligands	CLR, NA, OLA, ZMA

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5NM5 \| pdb_00005nm5	Download File View File

Tubulin Darpin room-temperature structure in complex with Colchicine determined by serial millisecond crystallography

Weinert, T., Olieric, N., James, D., Gashi, D., Nogly, P., Jaeger, K., Steinmetz, M.O., Standfuss, J.

(2017) Nat Commun 8: 542-542

Released	2017-09-27
Method	X-RAY DIFFRACTION 2.05 Å
Organisms	Bos taurus synthetic construct
Macromolecule	Designed Ankyrin Repeat Protein (DARPIN) D1 (protein) Tubulin alpha-1B chain (protein) Tubulin beta-2B chain (protein)
Unique Ligands	GDP, GTP, LOC, MG

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5NQT \| pdb_00005nqt	Download File View File

Tubulin Darpin room-temperature structure determined by serial millisecond crystallography

Weinert, T., Olieric, N., James, D., Gashi, D., Nogly, P., Jaeger, K., Steinmetz, M.O., Standfuss, J.

(2017) Nat Commun 8: 542-542

Released	2017-09-27
Method	X-RAY DIFFRACTION 2.15 Å
Organisms	Bos taurus synthetic construct
Macromolecule	DESIGNED ANKYRIN REPEAT PROTEIN (DARPIN) D1 (protein) Tubulin alpha-1B chain (protein) Tubulin beta-2B chain (protein)
Unique Ligands	GDP, GTP, MG

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5NQU \| pdb_00005nqu	Download File View File

Tubulin Darpin cryo structure

Weinert, T., Olieric, N., James, D., Gashi, D., Nogly, P., Jaeger, K., Steinmetz, M.O., Standfuss, J.

(2017) Nat Commun 8: 542-542

Released	2017-09-27
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Bos taurus synthetic construct
Macromolecule	Designed Ankyrin Repeat Protein (DARPIN) D1 (protein) Tubulin alpha-1B chain (protein) Tubulin beta-2B chain (protein)
Unique Ligands	GDP, GTP, MG

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5O5W \| pdb_00005o5w	Download File View File

Molybdenum storage protein room-temperature structure determined by serial millisecond crystallography

Steffen, B., Weinert, T., Ermler, U., Standfuss, J.

(2017) Nat Commun 8: 542-542

Released	2017-09-27
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Azotobacter vinelandii DJ
Macromolecule	Molybdenum storage protein subunit alpha (protein) Molybdenum storage protein subunit beta (protein)
Unique Ligands	8M0, ATP, M10, MG, MO

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5YM0 \| pdb_00005ym0	Download File View File

The crystal structure of DHAD

Zang, X., Huang, W.X., Cheng, R., Wu, L., Zhou, J.H., Tang, Y., Yan, Y.

To be published

Released	2018-10-24
Method	X-RAY DIFFRACTION 1.842 Å
Organisms	Arabidopsis thaliana
Macromolecule	Dihydroxy-acid dehydratase, chloroplastic (protein)
Unique Ligands	SO4

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5Z0Q \| pdb_00005z0q	Download File View File

Crystal Structure of OvoB

Cai, Y.J., Huang, P., Wu, L., Zhou, J.H., Liu, P.H.

(2018) Org Lett 20: 5427-5430

Released	2018-11-07
Method	X-RAY DIFFRACTION 2.77 Å
Organisms	Erwinia tasmaniensis Et1/99
Macromolecule	Aminotransferase, class I and II (protein)
Unique Ligands	PLP

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6KTV \| pdb_00006ktv	Download File View File

The structure of EanB complex with hercynine and persulfided Cys412

Wu, L., Liu, P.H., Zhou, J.H.

(2020) ACS Catal 10: 8981-8994

Released	2020-08-26
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Chlorobium limicola
Macromolecule	Sulfurtransferase (protein)
Unique Ligands	AVJ, CL, EDO, GOL, IMD, MG, NI, PDO, PEG, PG4

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6KTW \| pdb_00006ktw	Download File View File

structure of EanB with hercynine

Wu, L., Liu, P.H., Zhou, J.H.

(2020) ACS Catal 10: 8981-8994

Released	2020-08-26
Method	X-RAY DIFFRACTION 1.931 Å
Organisms	Chlorobium limicola
Macromolecule	Sulfurtransferase (protein)
Unique Ligands	AVJ, CL, EDO, GOL, IMD, MG, NA, PGE

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6KTX \| pdb_00006ktx	Download File View File

The wildtype structure of EanB

Wu, L., Liu, P.H., Zhou, J.H.

(2020) ACS Catal 10: 8981-8994

Released	2020-08-26
Method	X-RAY DIFFRACTION 2.189 Å
Organisms	Chlorobium limicola
Macromolecule	Sulfurtransferase (protein)
Unique Ligands	CL, EDO, MG, MPO, PEG, PGE

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6KTZ \| pdb_00006ktz	Download File View File

The complex structure of EanB/C412S with hercynine

Wu, L., Liu, P.H., Zhou, J.H.

(2020) ACS Catal 10: 8981-8994

Released	2020-08-26
Method	X-RAY DIFFRACTION 2 Å
Organisms	Chlorobium limicola
Macromolecule	Sulfurtransferase (protein)
Unique Ligands	AVJ, BR, CL, EDO, MG, PEG

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6KU1 \| pdb_00006ku1	Download File View File

The structure of EanB/Y353A complex with ergothioneine

Wu, L., Liu, P.H., Zhou, J.H.

(2020) ACS Catal 10: 8981-8994

Released	2020-08-26
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Chlorobium limicola
Macromolecule	Sulfurtransferase (protein)
Unique Ligands	CL, EDO, LW8, MG

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6KU2 \| pdb_00006ku2	Download File View File

The structure of EanB/Y353A complex with ergothioneine covalent linked with persulfide Cys412

Wu, L., Liu, P.H., Zhou, J.H.

(2020) ACS Catal 10: 8981-8994

Released	2020-08-26
Method	X-RAY DIFFRACTION 2.34 Å
Organisms	Chlorobium limicola
Macromolecule	Sulfurtransferase (protein)
Unique Ligands	BR, CL, DV6, EDO, GOL, IMD, MG, PEG, ZN

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6O6L \| pdb_00006o6l	Download File View File

The Structure of EgtB(Cabther) in complex with Hercynine

Irani, S., Zhang, Y.

(2019) ACS Catal 9: 6955-6961

Released	2019-07-31
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Chloracidobacterium thermophilum B
Macromolecule	EgtB (Cabther) (protein)
Unique Ligands	AVJ, FE

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6O6M \| pdb_00006o6m	Download File View File

The Structure of EgtB (Cabther)

Irani, S., Zhang, Y.

(2019) ACS Catal 9: 6955-6961

Released	2019-07-31
Method	X-RAY DIFFRACTION 2.506 Å
Organisms	Chloracidobacterium thermophilum B
Macromolecule	EgtB (Cabther) (protein)
Unique Ligands	FE, GOL

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6S0L \| pdb_00006s0l	Download File View File

Structure of the A2A adenosine receptor determined at SwissFEL using native-SAD at 4.57 keV from all available diffraction patterns

Nass, K., Cheng, R., Vera, L., Mozzanica, A., Redford, S., Ozerov, D., Basu, S., James, D., Knopp, G., Cirelli, C., Martiel, I., Casadei, C., Weinert, T., Nogly, P., Skopintsev, P., Usov, I., Leonarski, F., Geng, T., Rappas, M., Dore, A.S., Cooke, R., Nasrollahi Shirazi, S., Dworkowski, F., Sharpe, M., Olieric, N., Steinmetz, M.O., Schertler, G., Abela, R., Patthey, L., Schmitt, B., Hennig, M., Standfuss, J., Wang, M., Milne, J.C.

(2020) IUCrJ 7: 965-975

Released	2020-07-15
Method	X-RAY DIFFRACTION 2.65 Å
Organisms	Homo sapiens
Macromolecule	A2a adenosine receptor (protein)
Unique Ligands	CLR, OLA, OLB, OLC, ZMA

1 to 25 of 60 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

3FHR | pdb_00003fhr

3RVB | pdb_00003rvb

4AUA | pdb_00004aua

4EZ5 | pdb_00004ez5

4WXP | pdb_00004wxp

4WXR | pdb_00004wxr

5NJM | pdb_00005njm

5NLX | pdb_00005nlx

5NM2 | pdb_00005nm2

5NM4 | pdb_00005nm4

5NM5 | pdb_00005nm5

5NQT | pdb_00005nqt

5NQU | pdb_00005nqu

5O5W | pdb_00005o5w

5YM0 | pdb_00005ym0

5Z0Q | pdb_00005z0q

6KTV | pdb_00006ktv

6KTW | pdb_00006ktw

6KTX | pdb_00006ktx

6KTZ | pdb_00006ktz

6KU1 | pdb_00006ku1

6KU2 | pdb_00006ku2

6O6L | pdb_00006o6l

6O6M | pdb_00006o6m

6S0L | pdb_00006s0l