6HEM
 
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2WX0
 | | TAB2 NZF DOMAIN IN COMPLEX WITH Lys63-linked di-ubiquitin, P21 | | 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 (2.4 Å) | | Cite: | Two-Sided Ubiquitin Binding Explains Specificity of the Tab2 Nzf Domain
Nat.Struct.Mol.Biol., 16, 2009
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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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2WWZ
 | | TAB2 NZF DOMAIN IN COMPLEX WITH Lys63-linked di-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: | 2019-07-31 | | Method: | X-RAY DIFFRACTION (1.4 Å) | | Cite: | Two-Sided Ubiquitin Binding Explains Specificity of the Tab2 Nzf Domain
Nat.Struct.Mol.Biol., 16, 2009
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2XK5
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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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5OE7
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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: | 2012-01-25 | | 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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3ZLZ
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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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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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5OHN
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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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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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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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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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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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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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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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1Z5M
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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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