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232,829 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Chemical ID(s) = AYE

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Search Summary

This query matches 54 Structures.

Refinements

Structure Determination Methodology

experimental (54)

Scientific Name of Source Organism

	Homo sapiens (44)
	Chlamydia trachomatis L2/434/Bu (3)
	Human betacoronavirus 2c EMC/2012 (3)
	Mus musculus (3)
	Severe acute respiratory syndrome-related coronavirus (3)
	Bradyrhizobium (2)
	Burkholderia pseudomallei (2)
	Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (2)
	Ovis aries (2)
	Severe acute respiratory syndrome coronavirus 2 (2)

More...

Taxonomy

	Eukaryota (53)
	Bacteria (15)
	Riboviria (14)
	other sequences (1)
	unclassified viruses (1)

Experimental Method

X-RAY DIFFRACTION (54)

Polymer Entity Type

Protein (54)

Refinement Resolution (Å)

	1.0 - 1.5 (2)
	1.5 - 2.0 (14)
	2.0 - 2.5 (14)
	2.5 - 3.0 (15)
	3.0 - 3.5 (6)
	3.5 - 4.0 (3)

Release Date

	2005 - 2009 (1)
	2010 - 2014 (1)
	2015 - 2019 (26)
	2020 - 2024 (26)

Enzyme Classification Name

	Hydrolases (32)
	Transferases (13)
	Ligases (1)

Symmetry Type

	Asymmetric (49)
	Cyclic (5)

SCOP Classification

	Alpha and beta proteins (a+b) (29)
	Artifacts (7)

AllSelected

1 to 25 of 54 Structures

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2ZYP	Download File View File

X-ray structure of hen egg-white lysozyme with poly(allyl amine)

Ito, L., Tomita, S., Yamaguchi, H., Shiraki, K.

To be published

Released	2009-02-17
Method	X-RAY DIFFRACTION 1.18 Å
Organisms	Gallus gallus
Macromolecule	Lysozyme C (protein)
Unique Ligands	AYE, CL, NA

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3ZNH	Download File View File

Crimean Congo Hemorrhagic Fever Virus OTU domain in complex with ubiquitin-propargyl.

Ekkebus, R., vanKasteren, S.I., Kulathu, Y., Scholten, A., Berlin, I., deJong, A., Goerdayal, G., Neefjes, J., Heck, A.J.R., Komander, D., Ovaa, H.

(2013) J Am Chem Soc 135: 2867

Released	2013-02-27
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Crimean-Congo hemorrhagic fever virus strain IbAr10200 Homo sapiens
Macromolecule	POLYUBIQUITIN-B (protein) UBIQUITIN THIOESTERASE (protein)

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4UEL	Download File View File

UCH-L5 in complex with ubiquitin-propargyl bound to the RPN13 DEUBAD domain

Sahtoe, D.D., Van Dijk, W.J., El Oualid, F., Ekkebus, R., Ovaa, H., Sixma, T.K.

(2015) Mol Cell 57: 887

Released	2015-03-04
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	POLYUBIQUITIN-B (protein) PROTEASOMAL UBIQUITIN RECEPTOR ADRM1 (protein) UBIQUITIN CARBOXYL-TERMINAL HYDROLASE ISOZYME L5 (protein)

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4UF6	Download File View File

UCH-L5 in complex with ubiquitin-propargyl bound to an activating fragment of INO80G

Sahtoe, D.D., Van Dijk, W.J., El Oualid, F., Ekkebus, R., Ovaa, H., Sixma, T.K.

(2015) Mol Cell 57: 887

Released	2015-03-04
Method	X-RAY DIFFRACTION 3.69 Å
Organisms	Homo sapiens
Macromolecule	NUCLEAR FACTOR RELATED TO KAPPA-B-BINDING PROTEIN (protein) POLYUBIQUITIN-B (protein) UBIQUITIN CARBOXYL-TERMINAL HYDROLASE ISOZYME L5 (protein)

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5CHV	Download File View File

Crystal structure of USP18-ISG15 complex

Fritz, G., Basters, A.

(2017) Nat Struct Mol Biol 24: 270-278

Released	2016-09-28
Method	X-RAY DIFFRACTION 3.005 Å
Organisms	Mus musculus
Macromolecule	Ubiquitin-like protein ISG15 (protein) Ubl carboxyl-terminal hydrolase 18 (protein)
Unique Ligands	CL, SO4, ZN

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5E6J	Download File View File

Structure of SARS PLpro bound to a Lys48-linked di-ubiquitin activity based probe

Lima, C.D., Bekes, M.

(2016) Mol Cell 62: 572-585

Released	2016-05-18
Method	X-RAY DIFFRACTION 2.85 Å
Organisms	Severe acute respiratory syndrome-related coronavirus synthetic construct
Macromolecule	Polyubiquitin-B (protein) Replicase polyprotein 1ab (protein) ubiquitin (protein)
Unique Ligands	ACT, NI

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5JP1	Download File View File

Structure of Xanthomonas campestris effector protein XopD bound to tomato SUMO

Pruneda, J.N., Komander, D.

(2016) Mol Cell 63: 261-276

Released	2016-07-27
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Solanum lycopersicum Xanthomonas euvesicatoria pv. vesicatoria str. 85-10
Macromolecule	Small ubiquitin-related modifier (protein) Xanthomonas outer protein D (protein)
Unique Ligands	D1D, MLI

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5JP3	Download File View File

Structure of Xanthomonas campestris effector protein XopD bound to ubiquitin

Pruneda, J.N., Komander, D.

(2016) Mol Cell 63: 261-276

Released	2016-07-27
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Homo sapiens Xanthomonas euvesicatoria pv. vesicatoria str. 85-10
Macromolecule	Polyubiquitin-B (protein) Xanthomonas outer protein D (protein)

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5JQS	Download File View File

Crystal structure of deubiquitinase MINDY-1 in complex with Ubiquitin

Abdul Rehman, S.A., Kulathu, Y.

(2016) Mol Cell 63: 146-155

Released	2016-06-22
Method	X-RAY DIFFRACTION 2.65 Å
Organisms	Bos taurus Homo sapiens
Macromolecule	Protein FAM63A (protein) Ubiquitin-40S ribosomal protein S27a (protein)
Unique Ligands	AYE, CL, DIO, SO4

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5JZE	Download File View File

Erve virus viral OTU domain protease in complex with mouse ISG15

Deaton, M.K., Dzimianski, J.V., Pegan, S.D.

(2016) J Virol 90: 8314-8327

Released	2016-10-19
Method	X-RAY DIFFRACTION 2.47 Å
Organisms	Erve virus Mus musculus
Macromolecule	RNA-dependent RNA polymerase (protein) Ubiquitin-like protein ISG15 (protein)
Unique Ligands	AYE, FLC

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5L8W	Download File View File

Structure of USP12-UB-PRG/UAF1

Dharadhar, S., Sixma, T.

(2016) J Struct Biol 196: 437-447

Released	2016-09-28
Method	X-RAY DIFFRACTION 2.79 Å
Organisms	Homo sapiens
Macromolecule	Polyubiquitin-B (protein) Ubiquitin carboxyl-terminal hydrolase 12 (protein) WD repeat-containing protein 48 (protein)
Unique Ligands	AYE, GOL, ZN

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5LRX	Download File View File

Structure of A20 OTU domain bound to ubiquitin

Mevissen, T.E.T., Kulathu, Y., Mulder, M.P.C., Geurink, P.P., Maslen, S.L., Gersch, M., Elliott, P.R., Burke, J.E., van Tol, B.D.M., Akutsu, M., El Oualid, F., Kawasaki, M., Freund, S.M.V., Ovaa, H., Komander, D.

(2016) Nature 538: 402-405

Released	2016-10-19
Method	X-RAY DIFFRACTION 2.85 Å
Organisms	Homo sapiens
Macromolecule	Polyubiquitin-B (protein) Tumor necrosis factor alpha-induced protein 3 (protein)

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5OHK	Download File View File

Crystal structure of USP30 in covalent complex with ubiquitin propargylamide (high resolution)

Gersch, M., Komander, D.

(2017) Nat Struct Mol Biol 24: 920-930

Released	2017-09-20
Method	X-RAY DIFFRACTION 2.34 Å
Organisms	Homo sapiens
Macromolecule	Polyubiquitin-B (protein) Ubiquitin carboxyl-terminal hydrolase 30,Ubiquitin carboxyl-terminal hydrolase 30,Ubiquitin carboxyl-terminal hydrolase 30 (protein)
Unique Ligands	AYE, ZN

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5OHN	Download File View File

Crystal structure of USP30 in covalent complex with ubiquitin propargylamide (low resolution)

Gersch, M., Komander, D.

(2017) Nat Struct Mol Biol 24: 920-930

Released	2017-09-20
Method	X-RAY DIFFRACTION 3.6 Å
Organisms	Homo sapiens
Macromolecule	Polyubiquitin-B (protein) Ubiquitin carboxyl-terminal hydrolase 30,Ubiquitin carboxyl-terminal hydrolase 30 (protein)
Unique Ligands	ZN

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5TL6	Download File View File

Crystal structure of SARS-CoV papain-like protease in complex with the C-terminal domain of human ISG15

Dzimianski, J.V., Daczkowski, C.M., Pegan, S.D.

(2017) J Mol Biology 429: 1661-1683

Released	2017-05-03
Method	X-RAY DIFFRACTION 2.618 Å
Organisms	Homo sapiens Severe acute respiratory syndrome-related coronavirus
Macromolecule	Replicase polyprotein 1ab (protein) Ubiquitin-like protein ISG15 (protein)
Unique Ligands	SO4, ZN

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5TL7	Download File View File

Crystal structure of SARS-CoV papain-like protease in complex with C-terminal domain mouse ISG15

Daczkowski, C.D., Dzimianski, J.V., Pegan, S.D.

(2017) J Mol Biology 429: 1661-1683

Released	2017-05-03
Method	X-RAY DIFFRACTION 2.44 Å
Organisms	Mus musculus Severe acute respiratory syndrome-related coronavirus
Macromolecule	Replicase polyprotein 1ab (protein) Ubiquitin-like protein ISG15 (protein)
Unique Ligands	ZN

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5W8T	Download File View File

Crystal structure of MERS-CoV papain-like protease in complex with the C-terminal domain of human ISG15

Daczkowski, C.M., Goodwin, O.Y., Dzimianski, J.V., Farhat, J.J., Pegan, S.D.

(2017) J Virol 91:

Released	2017-09-27
Method	X-RAY DIFFRACTION 2.758 Å
Organisms	Homo sapiens Human betacoronavirus 2c EMC/2012
Macromolecule	ORF1ab (protein) Ubiquitin-like protein ISG15 (protein)
Unique Ligands	AYE, MPD, ZN

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5W8U	Download File View File

Crystal structure of MERS-CoV papain-like protease in complex with the C-terminal domain of human ISG15

Daczkowski, C.M., Goodwin, O.Y., Dzimianski, J.D., Pegan, S.D.

(2017) J Virol 91:

Released	2017-09-27
Method	X-RAY DIFFRACTION 2.411 Å
Organisms	Homo sapiens Human betacoronavirus 2c EMC/2012
Macromolecule	ORF1ab (protein) Ubiquitin-like protein ISG15 (protein)
Unique Ligands	AYE, MPD, ZN

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6BI8	Download File View File

X-ray structure of MERS coronavirus papain-like protease in complex with human ISG15

Clasman, J.C., Mesecar, A.D.

(2020) Antiviral Res 174: 104661-104661

Released	2018-11-07
Method	X-RAY DIFFRACTION 2.291 Å
Organisms	Homo sapiens Human betacoronavirus 2c EMC/2012
Macromolecule	ORF1a (protein) Ubiquitin-like protein ISG15 (protein)
Unique Ligands	AYE, CIT, EDO, GOL, PGE, ZN

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6EI1	Download File View File

Crystal structure of the covalent complex between deubiquitinase ZUFSP (ZUP1) and Ubiquitin-PA

Pichlo, C., Baumann, U., Hofmann, K., Hermanns, T.

(2018) Nat Commun 9: 799-799

Released	2018-03-07
Method	X-RAY DIFFRACTION 1.732 Å
Organisms	Homo sapiens
Macromolecule	Polyubiquitin-B (protein) Zinc finger with UFM1-specific peptidase domain protein (protein)
Unique Ligands	AYE, GOL, MLI

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6FDK	Download File View File

Structure of Chlamydia trachomatis effector protein Cdu1 bound to ubiquitin

Ramirez, Y., Kisker, C.

(2018) ChemMedChem 13: 2014-2023

Released	2018-08-15
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Chlamydia trachomatis L2/434/Bu Homo sapiens
Macromolecule	Deubiquitinase and deneddylase Dub1 (protein) Polyubiquitin-B (protein)
Unique Ligands	AYE, CL

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6FFA	Download File View File

FMDV Leader protease bound to substrate ISG15

Swatek, K.N., Pruneda, J.N., Komander, D.

(2018) Proc Natl Acad Sci U S A 115: 2371-2376

Released	2018-02-21
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Foot-and-mouth disease virus Homo sapiens
Macromolecule	Lbpro (protein) Ubiquitin-like protein ISG15 (protein)
Unique Ligands	GOL, SO4

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6FGE	Download File View File

Crystal structure of human ZUFSP/ZUP1 in complex with ubiquitin

Kwasna, D., Abdul Rehman, S.A., Kulathu, Y.

(2018) Mol Cell 70: 150-164.e6

Released	2018-04-04
Method	X-RAY DIFFRACTION 1.74 Å
Organisms	Homo sapiens
Macromolecule	Polyubiquitin-B (protein) Zinc finger with UFM1-specific peptidase domain protein (protein)
Unique Ligands	ACT, EDO, FMT, GOL, MLI, NH4, PEG

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6GZS	Download File View File

Structure of Chlamydia trachomatis effector protein ChlaDUB1 bound to ubiquitin

Pruneda, J.N., Komander, D.

(2018) Nat Microbiol 3: 1377-1384

Released	2018-11-14
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Chlamydia trachomatis L2/434/Bu Homo sapiens
Macromolecule	Deubiquitinase and deneddylase Dub1 (protein) Polyubiquitin-B (protein)
Unique Ligands	AYE, GOL, SO4

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6H4H	Download File View File

Usp28 catalytic domain variant E593D in complex with UbPA

Klemm, T.A., Sauer, F., Kisker, C.

(2019) Mol Cell 74: 421

Released	2019-03-27
Method	X-RAY DIFFRACTION 3.5 Å
Organisms	Homo sapiens
Macromolecule	Polyubiquitin-B (protein) Ubiquitin carboxyl-terminal hydrolase 28 (protein)
Unique Ligands	AYE, SO4