7KEO
| Crystal structure of K29-linked di-ubiquitin in complex with synthetic antigen binding fragment | Descriptor: | PHOSPHATE ION, Synthetic antigen binding fragment, heavy chain, ... | Authors: | Yu, Y, Zheng, Q, Erramilli, S, Pan, M, Kossiakoff, A, Liu, L, Zhao, M. | Deposit date: | 2020-10-11 | Release date: | 2021-07-28 | Last modified: | 2024-04-03 | Method: | X-RAY DIFFRACTION (2.9 Å) | Cite: | K29-linked ubiquitin signaling regulates proteotoxic stress response and cell cycle. Nat.Chem.Biol., 17, 2021
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5VF0
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3A33
| UbcH5b~Ubiquitin Conjugate | Descriptor: | GLYCEROL, Ubiquitin, Ubiquitin-conjugating enzyme E2 D2 | Authors: | Sakata, E, Satoh, T, Yamamoto, S, Yamaguchi, Y, Yagi-Utsumi, M, Kurimoto, E, Wakatsuki, S, Kato, K. | Deposit date: | 2009-06-08 | Release date: | 2009-11-24 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Crystal Structure of UbcH5b~Ubiquitin Intermediate: Insight into the Formation of the Self-Assembled E2~Ub Conjugates Structure, 18, 2010
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4DM9
| The Crystal Structure of Ubiquitin Carboxy-terminal hydrolase L1 (UCHL1) bound to a tripeptide fluoromethyl ketone Z-VAE(OMe)-FMK | Descriptor: | Tripeptide fluoromethyl ketone inhibitor Z-VAE(OMe)-FMK, Ubiquitin carboxyl-terminal hydrolase isozyme L1 | Authors: | Davies, C.W, Chaney, J, Korbel, G, Ringe, D, Petsko, G.A, Ploegh, H, Das, C. | Deposit date: | 2012-02-07 | Release date: | 2012-05-23 | Last modified: | 2023-09-13 | Method: | X-RAY DIFFRACTION (2.35 Å) | Cite: | The co-crystal structure of ubiquitin carboxy-terminal hydrolase L1 (UCHL1) with a tripeptide fluoromethyl ketone (Z-VAE(OMe)-FMK). Bioorg.Med.Chem.Lett., 22, 2012
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8EDE
| Crystal structure of covalent inhibitor 2-chloro-N'-(N-(4-chlorophenyl)-N-methylglycyl)acetohydrazide bound to Ubiquitin C-terminal Hydrolase-L1 | Descriptor: | 2-[(4-chlorophenyl)-methyl-amino]-~{N}'-ethanoyl-ethanehydrazide, SULFATE ION, Ubiquitin carboxyl-terminal hydrolase isozyme L1 | Authors: | Patel, R, Imhoff, R, Flaherty, D, Das, C. | Deposit date: | 2022-09-04 | Release date: | 2023-09-20 | Last modified: | 2024-04-10 | Method: | X-RAY DIFFRACTION (1.799 Å) | Cite: | Covalent Fragment Screening and Optimization Identifies the Chloroacetohydrazide Scaffold as Inhibitors for Ubiquitin C-terminal Hydrolase L1. J.Med.Chem., 67, 2024
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6NXK
| Ubiquitin binding variants | Descriptor: | Anaphase-promoting complex subunit 2, Polyubiquitin-C | Authors: | Miller, D.J, Watson, E.R. | Deposit date: | 2019-02-08 | Release date: | 2020-01-15 | Last modified: | 2023-10-11 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Protein engineering of a ubiquitin-variant inhibitor of APC/C identifies a cryptic K48 ubiquitin chain binding site. Proc.Natl.Acad.Sci.USA, 116, 2019
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6ASR
| REV1 UBM2 domain complex with ubiquitin | Descriptor: | DNA repair protein REV1, NICKEL (II) ION, Ubiquitin | Authors: | Miller, D.J. | Deposit date: | 2017-08-25 | Release date: | 2018-06-20 | Last modified: | 2023-10-04 | Method: | X-RAY DIFFRACTION (2.356 Å) | Cite: | Structures of REV1 UBM2 Domain Complex with Ubiquitin and with a Small-Molecule that Inhibits the REV1 UBM2-Ubiquitin Interaction. J. Mol. Biol., 430, 2018
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7NS4
| Catalytic module of yeast Chelator-GID SR4 E3 ubiquitin ligase | Descriptor: | E3 ubiquitin-protein ligase RMD5, Protein FYV10, ZINC ION | Authors: | Sherpa, D, Chrustowicz, J, Prabu, J.R, Schulman, B.A. | Deposit date: | 2021-03-05 | Release date: | 2021-05-05 | Last modified: | 2021-06-16 | Method: | ELECTRON MICROSCOPY (3.9 Å) | Cite: | GID E3 ligase supramolecular chelate assembly configures multipronged ubiquitin targeting of an oligomeric metabolic enzyme. Mol.Cell, 81, 2021
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3H8V
| Human Ubiquitin-activating Enzyme 5 in Complex with ATP | Descriptor: | ADENOSINE-5'-TRIPHOSPHATE, Ubiquitin-like modifier-activating enzyme 5, ZINC ION | Authors: | Walker, J.R, Bacik, J.P, Rastgoo, N, Weigelt, J, Bountra, C, Edwards, A.M, Arrowsmith, C.H, Bochkarev, A, Dhe-Paganon, S, Structural Genomics Consortium (SGC) | Deposit date: | 2009-04-29 | Release date: | 2009-05-26 | Last modified: | 2023-09-06 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Crystal structure of the human ubiquitin-activating enzyme 5 (UBA5) bound to ATP: mechanistic insights into a minimalistic E1 enzyme. J.Biol.Chem., 285, 2010
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2FID
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2FIF
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2LZ6
| Distinct ubiquitin binding modes exhibited by sh3 domains: molecular determinants and functional implications | Descriptor: | CD2-associated protein, Ubiquitin | Authors: | Ortega-Roldan, J, Azuaga, A, Blackledge, M, Van Nuland, N. | Deposit date: | 2012-09-24 | Release date: | 2013-10-02 | Last modified: | 2024-05-15 | Method: | SOLUTION NMR | Cite: | Distinct Ubiquitin Binding Modes Exhibited by SH3 Domains: Molecular Determinants and Functional Implications. Plos One, 8, 2013
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5V1Y
| Crystal structure of the ternary RPN13 PRU-RPN2 (940-953)-ubiquitin complex | Descriptor: | 26S proteasome non-ATPase regulatory subunit 1, Proteasomal ubiquitin receptor ADRM1, Ubiquitin | Authors: | Hemmis, C.W, VanderLinden, R.T, Yao, T, Robinson, H, Hill, C.P. | Deposit date: | 2017-03-02 | Release date: | 2017-05-03 | Last modified: | 2023-10-04 | Method: | X-RAY DIFFRACTION (1.421 Å) | Cite: | Structure and energetics of pairwise interactions between proteasome subunits RPN2, RPN13, and ubiquitin clarify a substrate recruitment mechanism. J. Biol. Chem., 292, 2017
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2BGF
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6GHA
| USP15 catalytic domain structure | Descriptor: | Ubiquitin carboxyl-terminal hydrolase 15,Ubiquitin carboxyl-terminal hydrolase 15, ZINC ION | Authors: | Ward, S.J, Gratton, H.E, Caulton, S.G, Emsley, J, Dreveny, I. | Deposit date: | 2018-05-06 | Release date: | 2018-09-26 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (1.98 Å) | Cite: | The structure of the deubiquitinase USP15 reveals a misaligned catalytic triad and an open ubiquitin-binding channel. J. Biol. Chem., 293, 2018
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4NNJ
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5V1Z
| Crystal structure of the RPN13 PRU-RPN2 (932-953)-ubiquitin complex | Descriptor: | 26S proteasome non-ATPase regulatory subunit 1, Proteasomal ubiquitin receptor ADRM1, Ubiquitin | Authors: | Hemmis, C.W, VanderLinden, R.T, Yao, T, Robinson, H, Hill, C.P. | Deposit date: | 2017-03-02 | Release date: | 2017-05-03 | Last modified: | 2023-10-04 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Structure and energetics of pairwise interactions between proteasome subunits RPN2, RPN13, and ubiquitin clarify a substrate recruitment mechanism. J. Biol. Chem., 292, 2017
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8PQL
| K48-linked ubiquitin chain formation with a cullin-RING E3 ligase and Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2-donor UB-acceptor UB-SIL1 peptide | Descriptor: | 5-azanylpentan-2-one, Cullin-2, E3 ubiquitin-protein ligase RBX1, ... | Authors: | Liwocha, J, Prabu, J.R, Kleiger, G, Schulman, B.A. | Deposit date: | 2023-07-11 | Release date: | 2024-02-14 | Last modified: | 2024-04-17 | Method: | ELECTRON MICROSCOPY (3.76 Å) | Cite: | Mechanism of millisecond Lys48-linked poly-ubiquitin chain formation by cullin-RING ligases. Nat.Struct.Mol.Biol., 31, 2024
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6P9G
| Structure of USP5 zinc-finger ubiquitin binding domain co-crystallized with 2-(4-oxoquinazolin-3(4H)-yl)propanoic acid | Descriptor: | (2R)-2-(4-oxoquinazolin-3(4H)-yl)propanoic acid, UNKNOWN ATOM OR ION, Ubiquitin carboxyl-terminal hydrolase 5, ... | Authors: | Tempel, W, Mann, M.K, Harding, R.J, Bountra, C, Arrowsmith, C.H, Edwards, A.M, Schapira, M, Structural Genomics Consortium (SGC) | Deposit date: | 2019-06-10 | Release date: | 2019-09-18 | Last modified: | 2023-10-11 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Discovery of Small Molecule Antagonists of the USP5 Zinc Finger Ubiquitin-Binding Domain. J.Med.Chem., 62, 2019
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7JXV
| ANTH domain of CALM (clathrin-assembly lymphoid myeloid leukemia protein) bound to ubiquitin | Descriptor: | Phosphatidylinositol-binding clathrin assembly protein, Ubiquitin | Authors: | Pashkova, N, Gakhar, L, Schnicker, N.J, Piper, R.C. | Deposit date: | 2020-08-28 | Release date: | 2021-08-04 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (2.35 Å) | Cite: | ANTH domains within CALM, HIP1R, and Sla2 recognize ubiquitin internalization signals. Elife, 10, 2021
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4P5O
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1TTN
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2MCN
| Distinct ubiquitin binding modes exhibited by SH3 domains: molecular determinants and functional implications | Descriptor: | CD2-associated protein, Ubiquitin | Authors: | Ortega-Roldan, J, Salmon, L, Azuaga, A, Blackledge, M, Van Nuland, N. | Deposit date: | 2013-08-22 | Release date: | 2014-02-05 | Last modified: | 2024-05-15 | Method: | SOLUTION NMR | Cite: | Distinct ubiquitin binding modes exhibited by SH3 domains: molecular determinants and functional implications. Plos One, 8, 2013
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5K1B
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6FJ7
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