6HEK
| Structure of human USP28 bound to Ubiquitin-PA | Descriptor: | CHLORIDE ION, Polyubiquitin-B, TETRAETHYLENE GLYCOL, ... | Authors: | Gersch, M, Komander, D. | Deposit date: | 2018-08-20 | Release date: | 2019-03-27 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (3.03 Å) | Cite: | Distinct USP25 and USP28 Oligomerization States Regulate Deubiquitinating Activity. Mol.Cell, 74, 2019
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6HEH
| Structure of the catalytic domain of USP28 (insertion deleted) | Descriptor: | 1,2-ETHANEDIOL, CHLORIDE ION, Ubiquitin carboxyl-terminal hydrolase 28,Ubiquitin carboxyl-terminal hydrolase 28 | Authors: | Gersch, M, Komander, D. | Deposit date: | 2018-08-20 | Release date: | 2019-03-27 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (2.26 Å) | Cite: | Distinct USP25 and USP28 Oligomerization States Regulate Deubiquitinating Activity. Mol.Cell, 74, 2019
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6HEI
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6HEL
| Structure of human USP25 | Descriptor: | Ubiquitin carboxyl-terminal hydrolase 25 | Authors: | Gersch, M, Komander, D. | Deposit date: | 2018-08-20 | Release date: | 2019-03-27 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (2.941 Å) | Cite: | Distinct USP25 and USP28 Oligomerization States Regulate Deubiquitinating Activity. Mol.Cell, 74, 2019
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6I9C
| Structure of the OTU domain of OTULIN G281R mutant | Descriptor: | CHLORIDE ION, GLYCEROL, Ubiquitin thioesterase otulin | Authors: | Damgaard, R.B, Elliott, P.R, Swatek, K.N, Maher, E.R, Stepensky, P, Elpeleg, O, Komander, D, Berkun, Y. | Deposit date: | 2018-11-22 | Release date: | 2019-03-06 | Last modified: | 2024-05-15 | Method: | X-RAY DIFFRACTION (1.77 Å) | Cite: | OTULIN deficiency in ORAS causes cell type-specific LUBAC degradation, dysregulated TNF signalling and cell death. Embo Mol Med, 11, 2019
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2WX1
| TAB2 NZF DOMAIN IN COMPLEX WITH Lys63-linked tri-ubiquitin, P212121 | Descriptor: | MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 7-INTERACTING PROTEIN 2, UBIQUITIN, ZINC ION | Authors: | Kulathu, Y, Akutsu, M, Bremm, A, Hofmann, K, Komander, D. | Deposit date: | 2009-10-30 | Release date: | 2009-11-24 | Last modified: | 2011-07-13 | Method: | X-RAY DIFFRACTION (3 Å) | Cite: | Two-Sided Ubiquitin Binding Explains Specificity of the Tab2 Nzf Domain Nat.Struct.Mol.Biol., 16, 2009
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3VVV
| Skich domain of NDP52 | Descriptor: | Calcium-binding and coiled-coil domain-containing protein 2 | Authors: | Akutsu, M, Muhlinen, N.V, Randow, F, Komander, D. | Deposit date: | 2012-07-28 | Release date: | 2013-02-27 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (1.35 Å) | Cite: | LC3C, bound selectively by a noncanonical LIR motif in NDP52, is required for antibacterial autophagy Mol.Cell, 48, 2012
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3VVW
| NDP52 in complex with LC3C | Descriptor: | Calcium-binding and coiled-coil domain-containing protein 2, Microtubule-associated proteins 1A/1B light chain 3C | Authors: | Akutsu, M, Muhlinen, N.V, Randow, F, Komander, D. | Deposit date: | 2012-07-28 | Release date: | 2013-02-27 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | LC3C, bound selectively by a noncanonical LIR motif in NDP52, is required for antibacterial autophagy Mol.Cell, 48, 2012
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3ZNH
| Crimean Congo Hemorrhagic Fever Virus OTU domain in complex with ubiquitin-propargyl. | Descriptor: | POLYUBIQUITIN-B, UBIQUITIN THIOESTERASE | Authors: | 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. | Deposit date: | 2013-02-14 | Release date: | 2013-02-27 | Last modified: | 2023-12-20 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | On Terminal Alkynes that Can React with Active-Site Cysteine Nucleophiles in Proteases. J.Am.Chem.Soc., 135, 2013
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3ZLZ
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3ZRH
| Crystal structure of the Lys29, Lys33-linkage-specific TRABID OTU deubiquitinase domain reveals an Ankyrin-repeat ubiquitin binding domain (AnkUBD) | Descriptor: | 1,2-ETHANEDIOL, CHLORIDE ION, UBIQUITIN THIOESTERASE ZRANB1 | Authors: | Licchesi, J.D.F, Akutsu, M, Komander, D. | Deposit date: | 2011-06-16 | Release date: | 2011-12-14 | Last modified: | 2024-05-08 | Method: | X-RAY DIFFRACTION (2.23 Å) | Cite: | An Ankyrin-Repeat Ubiquitin-Binding Domain Determines Trabid'S Specificity for Atypical Ubiquitin Chains. Nat.Struct.Mol.Biol., 19, 2011
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5NGE
| Crystal structure of USP7 in complex with the non-covalent inhibitor, FT671 | Descriptor: | 5-[[1-[(3~{S})-4,4-bis(fluoranyl)-3-(3-fluoranylpyrazol-1-yl)butanoyl]-4-oxidanyl-piperidin-4-yl]methyl]-1-(4-fluorophenyl)pyrazolo[3,4-d]pyrimidin-4-one, Ubiquitin carboxyl-terminal hydrolase 7 | Authors: | Turnbull, A.P, Krajewski, W.W, Ioannidis, S, Kessler, B.M, Komander, D. | Deposit date: | 2017-03-17 | Release date: | 2017-10-18 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (2.35 Å) | Cite: | Molecular basis of USP7 inhibition by selective small-molecule inhibitors. Nature, 550, 2017
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5NGF
| Crystal structure of USP7 in complex with the covalent inhibitor, FT827 | Descriptor: | 1,2-ETHANEDIOL, Ubiquitin carboxyl-terminal hydrolase 7, ~{N}-[2-[4-[4-[(1-methyl-4-oxidanylidene-pyrazolo[3,4-d]pyrimidin-5-yl)methyl]-4-oxidanyl-piperidin-1-yl]carbonylphenyl]phenyl]ethanesulfonamide | Authors: | Krajewski, W.W, Turnbull, A.P, Ioannidis, S, Kessler, B.M, Komander, D. | Deposit date: | 2017-03-17 | Release date: | 2017-10-18 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (2.33 Å) | Cite: | Molecular basis of USP7 inhibition by selective small-molecule inhibitors. Nature, 550, 2017
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5OHP
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5OHK
| Crystal structure of USP30 in covalent complex with ubiquitin propargylamide (high resolution) | Descriptor: | Polyubiquitin-B, Ubiquitin carboxyl-terminal hydrolase 30,Ubiquitin carboxyl-terminal hydrolase 30,Ubiquitin carboxyl-terminal hydrolase 30, ZINC ION, ... | Authors: | Gersch, M, Komander, D. | Deposit date: | 2017-07-17 | Release date: | 2017-09-20 | Last modified: | 2024-02-07 | Method: | X-RAY DIFFRACTION (2.34 Å) | Cite: | Mechanism and regulation of the Lys6-selective deubiquitinase USP30. Nat. Struct. Mol. Biol., 24, 2017
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5OHV
| K33-specific affimer bound to K33 diUb | Descriptor: | GLYCEROL, K33-specific affimer, SULFATE ION, ... | Authors: | Michel, M.A, Komander, D. | Deposit date: | 2017-07-18 | Release date: | 2017-10-04 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (2.801 Å) | Cite: | Ubiquitin Linkage-Specific Affimers Reveal Insights into K6-Linked Ubiquitin Signaling. Mol. Cell, 68, 2017
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5OHN
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5OHL
| K6-specific affimer bound to K6 diUb | Descriptor: | GLYCEROL, K6-specific affimer, POLYETHYLENE GLYCOL (N=34), ... | Authors: | Michel, M.A, Komander, D. | Deposit date: | 2017-07-17 | Release date: | 2017-10-04 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Ubiquitin Linkage-Specific Affimers Reveal Insights into K6-Linked Ubiquitin Signaling. Mol. Cell, 68, 2017
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5OHM
| K33-specific affimer bound to K33 diUb | Descriptor: | K33-specific affimer, POLYETHYLENE GLYCOL (N=34), Polyubiquitin-C | Authors: | Michel, M.A, Komander, D. | Deposit date: | 2017-07-17 | Release date: | 2017-10-04 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (3.8 Å) | Cite: | Ubiquitin Linkage-Specific Affimers Reveal Insights into K6-Linked Ubiquitin Signaling. Mol. Cell, 68, 2017
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5OXI
| C-terminally retracted ubiquitin L67S mutant | Descriptor: | SULFATE ION, Ubiquitin L67S mutant | Authors: | Gladkova, C.G, Schubert, A.F, Wagstaff, J.L, Pruneda, J.N, Freund, S.M.V, Komander, D. | Deposit date: | 2017-09-06 | Release date: | 2017-11-22 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (1.63 Å) | Cite: | An invisible ubiquitin conformation is required for efficient phosphorylation by PINK1. EMBO J., 36, 2017
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5OXH
| C-terminally retracted ubiquitin T66V/L67N mutant | Descriptor: | SULFATE ION, Ubiquitin T66V/L67N mutant | Authors: | Gladkova, C, Schubert, A.F, Wagstaff, J.L, Pruneda, J.P, Freund, S.M.V, Komander, D. | Deposit date: | 2017-09-06 | Release date: | 2017-11-22 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (1.601 Å) | Cite: | An invisible ubiquitin conformation is required for efficient phosphorylation by PINK1. EMBO J., 36, 2017
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8VEC
| Deep Mutational Scanning of SARS-CoV-2 PLpro | Descriptor: | Papain-like protease nsp3, ZINC ION | Authors: | Wu, X, Nguyen, J.V, Call, M.E, Call, M.J. | Deposit date: | 2023-12-18 | Release date: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Mutational Profiling of SARS-CoV-2 PLpro in human cells reveals requirements for function, structure, and drug escape Biorxiv, 2024
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6AQR
| SAGA DUB module Ubp8(C146A)/Sgf11/Sus1/Sgf73 bound to monoubiquitin | Descriptor: | Polyubiquitin-C, SAGA-associated factor 11, SAGA-associated factor 73, ... | Authors: | Morrow, M.E, Morgan, M.T, Wolberger, C. | Deposit date: | 2017-08-21 | Release date: | 2018-07-04 | Last modified: | 2023-10-04 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Active site alanine mutations convert deubiquitinases into high-affinity ubiquitin-binding proteins. EMBO Rep., 19, 2018
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2PE0
| CRYSTAL STRUCTURE OF HUMAN PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE 1 (PDK1) 5-Hydroxy-3-[1-(1H-pyrrol-2-yl)-eth-(Z)-ylidene]-1,3-dihydro-indol-2-one COMPLEX | Descriptor: | 3-phosphoinositide-dependent protein kinase 1, 5-HYDROXY-3-[(1R)-1-(1H-PYRROL-2-YL)ETHYL]-2H-INDOL-2-ONE, GLYCEROL, ... | Authors: | Whitlow, M, Adler, M. | Deposit date: | 2007-04-01 | Release date: | 2007-06-12 | Last modified: | 2011-07-13 | Method: | X-RAY DIFFRACTION (2.35 Å) | Cite: | Indolinone based phosphoinositide-dependent kinase-1 (PDK1) inhibitors. Part 1: Design, synthesis and biological activity. Bioorg.Med.Chem.Lett., 17, 2007
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2PE2
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