PDB: 1544 resultsInfo pagesStatus searchChemie searchBIRD

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6C16	Ubiquitin variant (UbV.Fbl10.1) bound to a human Skp1-Fbl11 fragment complex. Descriptor: Lysine-specific demethylase 2A, Polyubiquitin-B, S-phase kinase-associated protein 1 Authors: Manczyk, N, Sicheri, F. Deposit date: 2018-01-04 Release date: 2018-07-18 Last modified: 2023-10-04 Method: X-RAY DIFFRACTION (3.27 Å) Cite: A Structure-Based Strategy for Engineering Selective Ubiquitin Variant Inhibitors of Skp1-Cul1-F-Box Ubiquitin Ligases. Structure, 26, 2018
4I6L	Crystal structure of OTUB1 in complex with ubiquitin variant Descriptor: Ubiquitin, Ubiquitin thioesterase OTUB1 Authors: Juang, Y.C, Sicheri, F. Deposit date: 2012-11-29 Release date: 2013-01-16 Last modified: 2023-09-20 Method: X-RAY DIFFRACTION (2.488 Å) Cite: A strategy for modulation of enzymes in the ubiquitin system. Science, 339, 2013
5B83	Crystal structure of Optineurin UBAN in complex with linear ubiquitin Descriptor: Optineurin, tetra ubiquitin Authors: Ishii, R, Nureki, O. Deposit date: 2016-06-12 Release date: 2016-09-07 Last modified: 2023-11-08 Method: X-RAY DIFFRACTION (2.694 Å) Cite: Linear ubiquitination is involved in the pathogenesis of optineurin-associated amyotrophic lateral sclerosis Nat Commun, 7, 2016
5ZQ7	SidE-Ubi-NAD Descriptor: ADENOSINE MONOPHOSPHATE, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, SidE, ... Authors: Wang, Y, Gao, A, Gao, P. Deposit date: 2018-04-17 Release date: 2018-05-23 Last modified: 2023-11-22 Method: X-RAY DIFFRACTION (2.847 Å) Cite: Structural Insights into Non-canonical Ubiquitination Catalyzed by SidE. Cell, 173, 2018
6CFP	CRYSTAL STRUCTURE OF POLYMERASE ACID PROTEIN (PA) FROM INFLUENZA A VIRUS, WILSON-SMITH/1933 (H1N1) BOUND TO FRAGMENT HIT BSI-70565 1-{1-[4-FLUOROPHENYL)METHYL]-2-METHYL-1H-IMIDAZOL-4-YL}ETHAN-1-ONE Descriptor: 1-{1-[(4-fluorophenyl)methyl]-2-methyl-1H-imidazol-4-yl}ethan-1-one, DIMETHYL SULFOXIDE, Ubiquitin-like protein SMT3,Polymerase acidic protein Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) Deposit date: 2018-02-15 Release date: 2018-04-11 Last modified: 2023-10-04 Method: X-RAY DIFFRACTION (2.45 Å) Cite: CRYSTAL STRUCTURE OF POLYMERASE ACID PROTEIN (PA) FROM INFLUENZA A VIRUS, WILSON-SMITH/1933 (H1N1) BOUND TO FRAGMENT HIT BSI-70565 1-{1-[4-FLUOROPHENYL)METHYL]-2-METHYL-1H-IMIDAZOL-4-YL}ETHAN-1-ONE To Be Published
4II3	Crystal structure of S. pombe Ubiquitin activating enzyme 1 (Uba1) in complex with ubiquitin and ATP/Mg Descriptor: ADENOSINE-5'-TRIPHOSPHATE, CALCIUM ION, MAGNESIUM ION, ... Authors: Olsen, S.K, Lima, C.D. Deposit date: 2012-12-19 Release date: 2013-02-13 Last modified: 2023-09-20 Method: X-RAY DIFFRACTION (2.9 Å) Cite: Structure of a ubiquitin E1-E2 complex: insights to E1-E2 thioester transfer. Mol.Cell, 49, 2013
4LJO	Structure of an active ligase (HOIP)/ubiquitin transfer complex Descriptor: E3 ubiquitin-protein ligase RNF31, IMIDAZOLE, Polyubiquitin-C, ... Authors: Rana, R.R, Stieglitz, B, Koliopoulos, M.G, Morris-Davies, A.C, Christodoulou, E, Howell, S, Brown, N.R, Rittinger, K. Deposit date: 2013-07-05 Release date: 2013-10-16 Last modified: 2023-09-20 Method: X-RAY DIFFRACTION (1.564 Å) Cite: Structural basis for ligase-specific conjugation of linear ubiquitin chains by HOIP. Nature, 503, 2013
6B7M	Crystal structure of Legionella effector sdeD (lpg2509) in complex with Ubiquitin Descriptor: Polyubiquitin-C, SdeD (lpg2509) Authors: Mao, Y, Akturk, A, Wasilko, J. Deposit date: 2017-10-04 Release date: 2018-04-18 Last modified: 2024-03-13 Method: X-RAY DIFFRACTION (1.7 Å) Cite: Mechanism of phosphoribosyl-ubiquitination mediated by a single Legionella effector. Nature, 557, 2018
5BZ0	Crystal structure of IBV papain-like protease PLpro C101S mutant in complex with ubiquitin Descriptor: Replicase polyprotein 1ab, Ubiquitin-40S ribosomal protein S27a, ZINC ION Authors: Kong, L.Y, Yan, L.M, Zhang, Y, Rao, Z.H. Deposit date: 2015-06-11 Release date: 2016-06-15 Last modified: 2023-11-15 Method: X-RAY DIFFRACTION (2.1 Å) Cite: Crystal structure of IBV papain-like protease PLpro C101S mutant in complex with ubiquitin To Be Published
4LCD	Structure of an Rsp5xUbxSna3 complex: Mechanism of ubiquitin ligation and lysine prioritization by a HECT E3 Descriptor: E3 ubiquitin-protein ligase RSP5, Protein SNA3, Ubiquitin Authors: Kamadurai, H.B, Miller, D, Schulman, B.A. Deposit date: 2013-06-21 Release date: 2013-08-14 Last modified: 2024-02-28 Method: X-RAY DIFFRACTION (3.1 Å) Cite: Mechanism of ubiquitin ligation and lysine prioritization by a HECT E3. Elife, 2, 2013
5E6J	Structure of SARS PLpro bound to a Lys48-linked di-ubiquitin activity based probe Descriptor: ACETATE ION, NICKEL (II) ION, Polyubiquitin-B, ... Authors: Lima, C.D, Bekes, M. Deposit date: 2015-10-09 Release date: 2016-05-18 Last modified: 2023-11-15 Method: X-RAY DIFFRACTION (2.85 Å) Cite: Recognition of Lys48-Linked Di-ubiquitin and Deubiquitinating Activities of the SARS Coronavirus Papain-like Protease. Mol. Cell, 62, 2016
4LJP	Structure of an active ligase (HOIP-H889A)/ubiquitin transfer complex Descriptor: E3 ubiquitin-protein ligase RNF31, Polyubiquitin-C, ZINC ION Authors: Rana, R.R, Stieglitz, B, Koliopoulos, M.G, Morris-Davies, A.C, Christodoulou, E, Howell, S, Brown, N.R, Rittinger, K. Deposit date: 2013-07-05 Release date: 2013-10-16 Last modified: 2023-09-20 Method: X-RAY DIFFRACTION (2.15 Å) Cite: Structural basis for ligase-specific conjugation of linear ubiquitin chains by HOIP. Nature, 503, 2013
7SOL	Crystal Structures of the bispecific ubiquitin/FAT10 activating enzyme, Uba6 Descriptor: ADENOSINE MONOPHOSPHATE, INOSITOL HEXAKISPHOSPHATE, Ubiquitin, ... Authors: Olsen, S.K, Gao, F, Lv, Z. Deposit date: 2021-10-31 Release date: 2022-11-02 Last modified: 2024-04-17 Method: X-RAY DIFFRACTION (2.25000644 Å) Cite: Crystal structures reveal catalytic and regulatory mechanisms of the dual-specificity ubiquitin/FAT10 E1 enzyme Uba6. Nat Commun, 13, 2022
7TV4	Crystal structure of NEMO CoZi in complex with HOIP NZF1 and linear diubiquitin Descriptor: E3 ubiquitin-protein ligase RNF31, NF-kappa-B essential modulator, Polyubiquitin-C, ... Authors: Rahighi, S, Iyer, M, Oveisi, H. Deposit date: 2022-02-03 Release date: 2022-08-17 Last modified: 2023-10-18 Method: X-RAY DIFFRACTION (4.2 Å) Cite: Structural basis for the simultaneous recognition of NEMO and acceptor ubiquitin by the HOIP NZF1 domain. Sci Rep, 12, 2022
7US1	Structure of parkin (R0RB) bound to two phospho-ubiquitin molecules Descriptor: 1,2-ETHANEDIOL, DI(HYDROXYETHYL)ETHER, E3 ubiquitin-protein ligase parkin, ... Authors: Fakih, R, Sauve, V, Gehring, K. Deposit date: 2022-04-22 Release date: 2022-06-22 Last modified: 2023-10-18 Method: X-RAY DIFFRACTION (2.484 Å) Cite: Structure of the second phosphoubiquitin-binding site in parkin. J.Biol.Chem., 298, 2022
7UV5	The crystal structure of Papain-Like Protease of SARS CoV-2, C111S/D286N mutant, in complex with a Lys48-linked di-ubiquitin Descriptor: 1,2-ETHANEDIOL, Papain-like protease nsp3, Ubiquitin, ... Authors: Osipiuk, J, Tesar, C, Endres, M, Lanham, B.T, Wydorski, P, Fushman, D, Joachimiak, L, Joachimiak, A, Center for Structural Genomics of Infectious Diseases (CSGID) Deposit date: 2022-04-29 Release date: 2022-05-11 Last modified: 2023-10-25 Method: X-RAY DIFFRACTION (1.45 Å) Cite: Dual domain recognition determines SARS-CoV-2 PLpro selectivity for human ISG15 and K48-linked di-ubiquitin. Nat Commun, 14, 2023
9AZJ	Structure of ubiquitinated NEMO UBAN K285C-Ub G76C bound to HOIP NZF1 Descriptor: E3 ubiquitin-protein ligase RNF31, NF-kappa-B essential modulator, Ubiquitin, ... Authors: Michel, M.A, Scutts, S, Komander, D. Deposit date: 2024-03-11 Release date: 2024-07-31 Method: X-RAY DIFFRACTION (3.32 Å) Cite: Structure of TAB2 NZF domain bound to K6 / Lys6-linked diubiquitin To be published
9B0Z	Structure of Optineurin bound to HOIP NZF1 domain and M1-linked diubiquitin, crystal form 2 Descriptor: E3 ubiquitin-protein ligase RNF31, Optineurin, Ubiquitin, ... Authors: Michel, M.A, Scutts, S, Komander, D. Deposit date: 2024-03-12 Release date: 2024-07-31 Method: X-RAY DIFFRACTION (2.41 Å) Cite: Linkage and substrate specificity conferred by NZF ubiquitin binding domains To Be Published
9B12	Structure of Optineurin bound to HOIP NZF1 domain and M1-linked diubiquitin, crystal form 1 Descriptor: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, CHLORIDE ION, E3 ubiquitin-protein ligase RNF31, ... Authors: Michel, M.A, Scutts, S, Komander, D. Deposit date: 2024-03-12 Release date: 2024-07-31 Method: X-RAY DIFFRACTION (1.81 Å) Cite: Linkage and substrate specificity conferred by NZF ubiquitin binding domains To Be Published
8EHO	PRRSV-1 PLP2 domain bound to ubiquitin Descriptor: 3-AMINOPROPANE, GLYCEROL, NITRATE ION, ... Authors: Bailey-Elkin, B.A, Mark, B.L. Deposit date: 2022-09-14 Release date: 2023-12-06 Last modified: 2024-01-03 Method: X-RAY DIFFRACTION (2.85 Å) Cite: Demonstrating the importance of porcine reproductive and respiratory syndrome virus papain-like protease 2 deubiquitinating activity in viral replication by structure-guided mutagenesis. Plos Pathog., 19, 2023
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
9EQJ	Crystal structure of pVHL:EloB:EloC in complex with MP-1-39 Descriptor: (2S,4R)-1-[(2R)-2-[(1-fluoranylcyclopropyl)carbonylamino]-3-methyl-3-[[cis-4-(morpholin-4-ylmethyl)cyclohexyl]methylsulfanyl]butanoyl]-N-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide, Elongin-B, Elongin-C, ... Authors: Kroupova, A, Pierri, M, Liu, X, Ciulli, A. Deposit date: 2024-03-21 Release date: 2024-08-28 Method: X-RAY DIFFRACTION (2.05 Å) Cite: Stereochemical inversion at a 1,4-cyclohexyl PROTAC linker fine-tunes conformation and binding affinity. Bioorg.Med.Chem.Lett., 110, 2024
7LTO	Nse5-6 complex Descriptor: Non-structural maintenance of chromosome element 5, Ubiquitin-like protein SMT3,DNA repair protein KRE29 chimera Authors: Yu, Y, Li, S.B, Zheng, S, Tangy, S, Koyi, C, Wan, B.B, Kung, H.H, Andrej, S, Alex, K, Patel, D.J, Zhao, X.L. Deposit date: 2021-02-19 Release date: 2021-05-19 Last modified: 2024-03-06 Method: ELECTRON MICROSCOPY (3.2 Å) Cite: Integrative analysis reveals unique structural and functional features of the Smc5/6 complex. Proc.Natl.Acad.Sci.USA, 118, 2021
9C5E	Covalent Complex Between Parkin Catalytic (Rcat) Domain and Ubiquitin Descriptor: 1.7.6 3-bromanylpropan-1-amine, E3 ubiquitin-protein ligase parkin, Ubiquitin, ... Authors: Connelly, E.M, Rintala-Dempsey, A.C, Gundogdu, M, Freeman, E.A, Koszela, J, Aguirre, J.D, Zhu, G, Kamarainen, O, Tadayon, R, Walden, H, Shaw, G.S. Deposit date: 2024-06-06 Release date: 2024-08-14 Method: SOLUTION NMR Cite: Capturing the catalytic intermediates of parkin ubiquitination. Proc.Natl.Acad.Sci.USA, 121, 2024
9EQM	Crystal structure of pVHL:EloB:EloC in complex with MP-1-21 Descriptor: (2S,4R)-1-[(2R)-2-[(1-fluoranylcyclopropyl)carbonylamino]-3-methyl-3-[[trans-4-(morpholin-4-ylmethyl)cyclohexyl]methylsulfanyl]butanoyl]-N-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide, Elongin-B, Elongin-C, ... Authors: Kroupova, A, Pierri, M, Liu, X, Ciulli, A. Deposit date: 2024-03-21 Release date: 2024-08-28 Method: X-RAY DIFFRACTION (2.19 Å) Cite: Stereochemical inversion at a 1,4-cyclohexyl PROTAC linker fine-tunes conformation and binding affinity. Bioorg.Med.Chem.Lett., 110, 2024

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