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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Enzyme Classification Number = 3.4.19.12

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Search Summary

This query matches 775 Structures.

Refinements

Structure Determination Methodology

experimental (775)

Scientific Name of Source Organism

	Homo sapiens (450)
	Severe acute respiratory syndrome coronavirus 2 (213)
	Saccharomyces cerevisiae S288C (41)
	synthetic construct (26)
	Saccharomyces cerevisiae (24)
	Severe acute respiratory syndrome-related coronavirus (22)
	Mus musculus (15)
	Bos taurus (7)
	Crimean-Congo hemorrhagic fever virus strain IbAr10200 (7)
	Caenorhabditis elegans (6)

More...

Taxonomy

	Eukaryota (516)
	Riboviria (268)
	Duplodnaviria (27)
	other sequences (26)
	Eukaryota (eukaryotes) (5)
	Bacteria (4)
	Archaea (1)
	Varidnaviria (1)

Experimental Method

	X-RAY DIFFRACTION (591)
	ELECTRON MICROSCOPY (143)
	SOLUTION NMR (41)
	NEUTRON DIFFRACTION (2)

Polymer Entity Type

	Protein (775)
	RNA (54)
	DNA (8)
	NA-hybrid (1)

Refinement Resolution (Å)

	0.5 - 1.0 (3)
	1.0 - 1.5 (83)
	1.5 - 2.0 (145)
	2.0 - 2.5 (173)
	2.5 - 3.0 (137)
	3.0 - 3.5 (92)
	3.5 - 4.0 (39)
	4.0 - 4.5 (24)
	> 4.5 (40)

Release Date

	1995 - 1999 (2)
	2000 - 2004 (15)
	2005 - 2009 (45)
	2010 - 2014 (120)
	2015 - 2019 (188)
	2020 - 2024 (381)
	2025 - 2029 (24)

Enzyme Classification Name

	Hydrolases (775)
	Transferases (123)
	Ligases (29)
	Lyases (26)
	Isomerases (4)

Symmetry Type

	Asymmetric (673)
	Cyclic (113)
	Dihedral (11)
	Tetrahedral (1)
	Icosahedral (1)

SCOP Classification

	Alpha and beta proteins (a+b) (182)
	Artifacts (62)
	Alpha and beta proteins (a/b) (25)
	All beta proteins (35)
	All alpha proteins (16)
	Small proteins (16)
	Coiled coil proteins (1)
	Peptides (1)

AllSelected

1 to 25 of 775 Structures

Page 1 of 31

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1CMX \| pdb_00001cmx	Download File View File

STRUCTURAL BASIS FOR THE SPECIFICITY OF UBIQUITIN C-TERMINAL HYDROLASES

Johnston, S.C., Riddle, S.M., Cohen, R.E., Hill, C.P.

(1999) EMBO J 18: 3877-3887

Released	1999-07-27
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Homo sapiens Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Macromolecule	PROTEIN (UBIQUITIN YUH1-UBAL) (protein)

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1IXD \| pdb_00001ixd	Download File View File

Solution structure of the CAP-GLY domain from human cylindromatosis tomour-suppressor CYLD

Saito, K., Koshiba, S., Kigawa, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

(2004) Structure 12: 1719-1728

Released	2002-12-19
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Cylindromatosis tumour-suppressor CYLD (protein)

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1NB8 \| pdb_00001nb8	Download File View File

Structure of the catalytic domain of USP7 (HAUSP)

Hu, M., Li, P., Li, M., Li, W., Yao, T., Wu, J.-W., Gu, W., Cohen, R.E., Shi, Y.

(2002) Cell 111: 1041-1054

Released	2003-01-07
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	Ubiquitin carboxyl-terminal hydrolase 7 (protein)

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1NBF \| pdb_00001nbf	Download File View File

Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde

Hu, M., Li, P., Li, M., Li, W., Yao, T., Wu, J.-W., Gu, W., Cohen, R.E., Shi, Y.

(2002) Cell 111: 1041-1054

Released	2003-01-07
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	Ubiquitin aldehyde (protein) Ubiquitin carboxyl-terminal hydrolase 7 (protein)

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1TFF \| pdb_00001tff	Download File View File

Structure of Otubain-2

Nanao, M.H., Tcherniuk, S.O., Chroboczek, J., Dideberg, O., Dessen, A., Balakirev, M.Y.

(2004) EMBO Rep 5: 783-788

Released	2004-08-03
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	Ubiquitin thiolesterase protein OTUB2 (protein)

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1UCH \| pdb_00001uch	Download File View File

DEUBIQUITINATING ENZYME UCH-L3 (HUMAN) AT 1.8 ANGSTROM RESOLUTION

Johnston, S.C., Larsen, C.N., Cook, W.J., Wilkinson, K.D., Hill, C.P.

(1997) EMBO J 16: 3787-3796

Released	1998-01-28
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens
Macromolecule	UBIQUITIN C-TERMINAL HYDROLASE UCH-L3 (protein)

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1UJ0 \| pdb_00001uj0	Download File View File

Crystal Structure of STAM2 SH3 domain in complex with a UBPY-derived peptide

Kaneko, T., Kumasaka, T., Ganbe, T., Sato, T., Miyazawa, K., Kitamura, N., Tanaka, N.

(2003) J Biological Chem 278: 48162-48168

Released	2003-12-23
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Mus musculus
Macromolecule	deubiquitinating enzyme UBPY (protein) signal transducing adaptor molecule (SH3 domain and ITAM motif) 2 (protein)
Unique Ligands	PO4

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1VDL \| pdb_00001vdl	Download File View File

Solution Structure of RSGI RUH-013, a UBA domain in Mouse cDNA

Doi-Katayama, Y., Hirota, H., Saito, K., Koshiba, S., Kigawa, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2004-09-23
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	Ubiquitin carboxyl-terminal hydrolase 25 (protein)

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1VEK \| pdb_00001vek	Download File View File

Solution Structure of RSGI RUH-011, a UBA Domain from Arabidopsis cDNA

Higuchi, Y., Abe, T., Hirota, H., Saito, K., Koshiba, S., Kigawa, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2004-09-30
Method	SOLUTION NMR
Organisms	Arabidopsis thaliana
Macromolecule	ubiquitin-specific protease 14, putative (protein)

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1VJV \| pdb_00001vjv	Download File View File

Crystal structure of Ubiquitin carboxyl-terminal hydrolase 6 (yfr010w) from Saccharomyces cerevisiae at 1.74 A resolution

Joint Center for Structural Genomics (JCSG)

To be published

Released	2004-09-21
Method	X-RAY DIFFRACTION 1.74 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Ubiquitin carboxyl-terminal hydrolase 6 (protein)

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1W6V \| pdb_00001w6v	Download File View File

Solution structure of the DUSP domain of hUSP15

De Jong, R.D., Ab, E., Diercks, T., Truffault, V., Daniels, M., Kaptein, R., Folkers, G.E.

(2006) J Biological Chem 281: 5026

Released	2006-01-12
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 15 (protein)

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1WGG \| pdb_00001wgg	Download File View File

Solution Structure of the N-terminal Ubiquitin-like Domain of Mouse Ubiquitin Specific Protease 14 (USP14)

Zhao, C., Tomizawa, T., Koshiba, S., Inoue, M., Kigawa, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2004-11-28
Method	SOLUTION NMR
Organisms	Mus musculus
Macromolecule	Ubiquitin carboxyl-terminal hydrolase 14 (protein)

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1WH0 \| pdb_00001wh0	Download File View File

Solution structure of the CS domain of human USP19

Nakanishi, T., Tochio, N., Koshiba, S., Inoue, M., Kigawa, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2004-11-28
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Ubiquitin carboxyl-terminal hydrolase 19 (protein)

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1WHB \| pdb_00001whb	Download File View File

Solution structure of the Rhodanese-like domain in human ubiquitin specific protease 8 (UBP8)

Saito, K., Koshiba, S., Inoue, M., Kigawa, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2004-11-28
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	KIAA0055 (protein)

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1WHL \| pdb_00001whl	Download File View File

Solution structure of the 1st CAP-Gly domain in human cylindromatosis tumor suppressor CYLD

Saito, K., Koshiba, S., Inoue, M., Kigawa, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2004-11-28
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Cylindromatosis tumor suppressor CYLD (protein)

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1WHM \| pdb_00001whm	Download File View File

Solution structure of the 2nd CAP-Gly domain in human cylindromatosis tumor suppressor CYLD

Saitok, K., Koshiba, S., Inoue, M., Kigawa, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2004-11-28
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Cylindromatosis tumor suppressor CYLD (protein)

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1WIV \| pdb_00001wiv	Download File View File

solution structure of RSGI RUH-023, a UBA domain from Arabidopsis cDNA

Higuchi, Y., Abe, T., Hirota, H., Izumi, K., Yoshida, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2004-11-28
Method	SOLUTION NMR
Organisms	Arabidopsis thaliana
Macromolecule	ubiquitin-specific protease 14 (protein)

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1XD3 \| pdb_00001xd3	Download File View File

Crystal structure of UCHL3-UbVME complex

Misaghi, S., Galardy, P.J., Meester, W.J.N., Ovaa, H., Ploegh, H.L., Gaudet, R.

(2005) J Biological Chem 280: 1512-1520

Released	2004-11-23
Method	X-RAY DIFFRACTION 1.45 Å
Organisms	Homo sapiens
Macromolecule	UBC protein (protein) Ubiquitin Carboxyl-terminal esterase L3 (protein)
Unique Ligands	GVE, MG

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1YY6 \| pdb_00001yy6	Download File View File

The Crystal Structure of the N-terminal domain of HAUSP/USP7 complexed with an EBNA1 peptide

Saridakis, V., Sheng, Y., Sarkari, F., Holowaty, M., Shire, K., Nguyen, T., Zhang, R., Liao, J., Lee, W., Edwards, A.M., Arrowsmith, C.H., Frappier, L.

(2005) Mol Cell 18: 25-36

Released	2005-04-05
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Epstein-Barr virus (strain B95-8) Homo sapiens
Macromolecule	Epstein-Barr nuclear antigen-1 (protein) Ubiquitin carboxyl-terminal hydrolase 7 (protein)
Unique Ligands	NA

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1YZB \| pdb_00001yzb	Download File View File

Solution structure of the Josephin domain of Ataxin-3

Nicastro, G., Masino, L., Menon, R.P., Knowles, P.P., McDonald, N.Q., Pastore, A.

(2005) Proc Natl Acad Sci U S A 102: 10493-10498

Released	2005-07-05
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Machado-Joseph disease protein 1 (protein)

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1YZE \| pdb_00001yze	Download File View File

Crystal structure of the N-terminal domain of USP7/HAUSP.

Saridakis, V., Sheng, Y., Sarkari, F., Holowaty, M.N., Shire, K., Nguyen, T., Zhang, R.G., Liao, J., Lee, W., Edwards, A.M., Arrowsmith, C.H., Frappier, L.

(2005) Mol Cell 18: 25-36

Released	2005-04-05
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	Ubiquitin carboxyl-terminal hydrolase 7 (protein)

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2A9U \| pdb_00002a9u	Download File View File

Structure of the N-terminal domain of Human Ubiquitin carboxyl-terminal hydrolase 8 (USP8)

Walker, J.R., Avvakumov, G.V., Xue, S., Newman, E.M., Mackenzie, F., Weigelt, J., Sundstrom, M., Arrowsmith, C., Edwards, E., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

(2006) J Biological Chem 281: 38061-38070

Released	2005-08-16
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Homo sapiens
Macromolecule	Ubiquitin carboxyl-terminal hydrolase 8 (protein)

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2AGA \| pdb_00002aga	Download File View File

De-ubiquitinating function of ataxin-3: insights from the solution structure of the Josephin domain

Mao, Y., Senic-Matuglia, F., Di Fiore, P., Polo, S., Hodsdon, M.E., De Camilli, P.

(2005) Proc Natl Acad Sci U S A 102: 12700-12705

Released	2005-08-30
Method	SOLUTION NMR
Organisms	Homo sapiens
Macromolecule	Machado-Joseph disease protein 1 (protein)

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2AYN \| pdb_00002ayn	Download File View File

Structure of USP14, a proteasome-associated deubiquitinating enzyme

Hu, M., Li, P., Jeffrey, P.D., Shi, Y.

(2005) EMBO J 24: 3747-3756

Released	2005-10-18
Method	X-RAY DIFFRACTION 3.2 Å
Organisms	Homo sapiens
Macromolecule	Ubiquitin carboxyl-terminal hydrolase 14 (protein)

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2AYO \| pdb_00002ayo	Download File View File

Structure of USP14 bound to ubquitin aldehyde

Hu, M., Li, P., Jeffrey, P.D., Shi, Y.

(2005) EMBO J 24: 3747-3756

Released	2005-10-18
Method	X-RAY DIFFRACTION 3.5 Å
Organisms	Homo sapiens
Macromolecule	Ubiquitin (protein) Ubiquitin carboxyl-terminal hydrolase 14 (protein)

1 to 25 of 775 Structures

Page 1 of 31

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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

1CMX | pdb_00001cmx

1IXD | pdb_00001ixd

1NB8 | pdb_00001nb8

1NBF | pdb_00001nbf

1TFF | pdb_00001tff

1UCH | pdb_00001uch

1UJ0 | pdb_00001uj0

1VDL | pdb_00001vdl

1VEK | pdb_00001vek

1VJV | pdb_00001vjv

1W6V | pdb_00001w6v

1WGG | pdb_00001wgg

1WH0 | pdb_00001wh0

1WHB | pdb_00001whb

1WHL | pdb_00001whl

1WHM | pdb_00001whm

1WIV | pdb_00001wiv

1XD3 | pdb_00001xd3

1YY6 | pdb_00001yy6

1YZB | pdb_00001yzb

1YZE | pdb_00001yze

2A9U | pdb_00002a9u

2AGA | pdb_00002aga

2AYN | pdb_00002ayn

2AYO | pdb_00002ayo