4WJ5
| Structure of HLA-A2 in complex with an altered peptide ligands based on Mart-1 variant epitope | Descriptor: | Beta-2-microglobulin, GLYCEROL, HLA class I histocompatibility antigen, ... | Authors: | Celie, P.H.N, Rodenko, B, Ovaa, H. | Deposit date: | 2014-09-29 | Release date: | 2014-10-29 | Last modified: | 2024-01-10 | Method: | X-RAY DIFFRACTION (1.65 Å) | Cite: | Altered Peptide Ligands Revisited: Vaccine Design through Chemically Modified HLA-A2-Restricted T Cell Epitopes. J Immunol., 193, 2014
|
|
1XD3
| Crystal structure of UCHL3-UbVME complex | Descriptor: | MAGNESIUM ION, METHYL 4-AMINOBUTANOATE, UBC protein, ... | Authors: | Misaghi, S, Galardy, P.J, Meester, W.J.N, Ovaa, H, Ploegh, H.L, Gaudet, R. | Deposit date: | 2004-09-03 | Release date: | 2004-11-23 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (1.45 Å) | Cite: | Structure of the Ubiquitin Hydrolase UCH-L3 Complexed with a Suicide Substrate J.Biol.Chem., 280, 2005
|
|
4UF6
| UCH-L5 in complex with ubiquitin-propargyl bound to an activating fragment of INO80G | Descriptor: | NUCLEAR FACTOR RELATED TO KAPPA-B-BINDING PROTEIN, POLYUBIQUITIN-B, UBIQUITIN CARBOXYL-TERMINAL HYDROLASE ISOZYME L5 | Authors: | Sahtoe, D.D, Van Dijk, W.J, El Oualid, F, Ekkebus, R, Ovaa, H, Sixma, T.K. | Deposit date: | 2014-12-23 | Release date: | 2015-03-04 | Last modified: | 2019-04-03 | Method: | X-RAY DIFFRACTION (3.69 Å) | Cite: | Mechanism of Uch-L5 Activation and Inhibition by Deubad Domains in Rpn13 and Ino80G. Mol.Cell, 57, 2015
|
|
4UEL
| UCH-L5 in complex with ubiquitin-propargyl bound to the RPN13 DEUBAD domain | Descriptor: | POLYUBIQUITIN-B, PROTEASOMAL UBIQUITIN RECEPTOR ADRM1, UBIQUITIN CARBOXYL-TERMINAL HYDROLASE ISOZYME L5 | Authors: | Sahtoe, D.D, Van Dijk, W.J, El Oualid, F, Ekkebus, R, Ovaa, H, Sixma, T.K. | Deposit date: | 2014-12-18 | Release date: | 2015-03-04 | Last modified: | 2019-04-03 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Mechanism of Uch-L5 Activation and Inhibition by Deubad Domains in Rpn13 and Ino80G. Mol.Cell, 57, 2015
|
|
4UF5
| Crystal structure of UCH-L5 in complex with inhibitory fragment of INO80G | Descriptor: | NUCLEAR FACTOR RELATED TO KAPPA-B-BINDING PROTEIN, UBIQUITIN CARBOXYL-TERMINAL HYDROLASE ISOZYME L5 | Authors: | Sahtoe, D.D, Van Dijk, W.J, El Oualid, F, Ekkebus, R, Ovaa, H, Sixma, T.K. | Deposit date: | 2014-12-23 | Release date: | 2015-03-04 | Last modified: | 2023-12-20 | Method: | X-RAY DIFFRACTION (3.7 Å) | Cite: | Mechanism of Uch-L5 Activation and Inhibition by Deubad Domains in Rpn13 and Ino80G. Mol.Cell, 57, 2015
|
|
4UEM
| UCH-L5 in complex with the RPN13 DEUBAD domain | Descriptor: | PROTEASOMAL UBIQUITIN RECEPTOR ADRM1, UBIQUITIN CARBOXYL-TERMINAL HYDROLASE ISOZYME L5 | Authors: | Sahtoe, D.D, Van Dijk, W.J, El Oualid, F, Ekkebus, R, Ovaa, H, Sixma, T.K. | Deposit date: | 2014-12-18 | Release date: | 2015-03-04 | Last modified: | 2023-12-20 | Method: | X-RAY DIFFRACTION (2.82 Å) | Cite: | Mechanism of Uch-L5 Activation and Inhibition by Deubad Domains in Rpn13 and Ino80G. Mol.Cell, 57, 2015
|
|
5LRV
| Structure of Cezanne/OTUD7B OTU domain bound to Lys11-linked diubiquitin | Descriptor: | GLYCEROL, OTU domain-containing protein 7B, PHOSPHATE ION, ... | Authors: | Mevissen, T.E.T, Kulathu, Y, Mulder, M.P.C, Geurink, P.P, Maslen, S.L, Gersch, M, Elliott, P.R, Burke, J.E, van Tol, B.D.M, Akutsu, M, El Oualid, F, Kawasaki, M, Freund, S.M.V, Ovaa, H, Komander, D. | Deposit date: | 2016-08-22 | Release date: | 2016-10-19 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Molecular basis of Lys11-polyubiquitin specificity in the deubiquitinase Cezanne. Nature, 538, 2016
|
|
5LRW
| Structure of Cezanne/OTUD7B OTU domain bound to ubiquitin | Descriptor: | GLYCEROL, OTU domain-containing protein 7B, Polyubiquitin-B | Authors: | Mevissen, T.E.T, Kulathu, Y, Mulder, M.P.C, Geurink, P.P, Maslen, S.L, Gersch, M, Elliott, P.R, Burke, J.E, van Tol, B.D.M, Akutsu, M, El Oualid, F, Kawasaki, M, Freund, S.M.V, Ovaa, H, Komander, D. | Deposit date: | 2016-08-22 | Release date: | 2016-10-19 | Last modified: | 2017-09-13 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Molecular basis of Lys11-polyubiquitin specificity in the deubiquitinase Cezanne. Nature, 538, 2016
|
|
5LRU
| Structure of Cezanne/OTUD7B OTU domain | Descriptor: | OTU domain-containing protein 7B | Authors: | Mevissen, T.E.T, Kulathu, Y, Mulder, M.P.C, Geurink, P.P, Maslen, S.L, Gersch, M, Elliott, P.R, Burke, J.E, van Tol, B.D.M, Akutsu, M, El Oualid, F, Kawasaki, M, Freund, S.M.V, Ovaa, H, Komander, D. | Deposit date: | 2016-08-22 | Release date: | 2016-10-19 | Last modified: | 2017-09-13 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Molecular basis of Lys11-polyubiquitin specificity in the deubiquitinase Cezanne. Nature, 538, 2016
|
|
5LRX
| Structure of A20 OTU domain bound to ubiquitin | Descriptor: | Polyubiquitin-B, Tumor necrosis factor alpha-induced protein 3 | Authors: | Mevissen, T.E.T, Kulathu, Y, Mulder, M.P.C, Geurink, P.P, Maslen, S.L, Gersch, M, Elliott, P.R, Burke, J.E, van Tol, B.D.M, Akutsu, M, El Oualid, F, Kawasaki, M, Freund, S.M.V, Ovaa, H, Komander, D. | Deposit date: | 2016-08-22 | Release date: | 2016-10-19 | Last modified: | 2017-09-13 | Method: | X-RAY DIFFRACTION (2.85 Å) | Cite: | Molecular basis of Lys11-polyubiquitin specificity in the deubiquitinase Cezanne. Nature, 538, 2016
|
|
5IFR
| Structure of the stable UBE2D3-UbDha conjugate | Descriptor: | GLYCEROL, Polyubiquitin-B, Ubiquitin-conjugating enzyme E2 D3 | Authors: | Pruneda, J.N, Mulder, M.P.C, Witting, K, Ovaa, H, Komander, D. | Deposit date: | 2016-02-26 | Release date: | 2016-05-11 | Last modified: | 2024-01-10 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | A cascading activity-based probe sequentially targets E1-E2-E3 ubiquitin enzymes. Nat.Chem.Biol., 12, 2016
|
|
2X4T
| Crystal structure of MHC CLass I HLA-A2.1 bound to a Peiodate- cleavable peptide | Descriptor: | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, 65 KDA PHOSPHOPROTEIN, BETA-2-MICROGLOBULIN, ... | Authors: | Rodenko, B, Toebes, M, Celie, P.H.N, Perrakis, A, Schumacher, T.N.M, Ovaa, H. | Deposit date: | 2010-02-02 | Release date: | 2010-03-02 | Last modified: | 2023-12-20 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Class I Major Histocompatibility Complexes Loaded by a Periodate Trigger. J.Am.Chem.Soc., 131, 2009
|
|
2X4Q
| Crystal structure of MHC CLass I HLA-A2.1 bound to a photocleavable peptide | Descriptor: | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, BETA-2-MICROGLOBULIN, GLYCEROL, ... | Authors: | Celie, P.H.N, Toebes, M, Rodenko, B, Ovaa, H, Perrakis, A, Schumacher, T.N.M. | Deposit date: | 2010-02-02 | Release date: | 2010-03-02 | Last modified: | 2023-12-20 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | Class I Major Histocompatibility Complexes Loaded by a Periodate Trigger. J.Am.Chem.Soc., 131, 2009
|
|
2X4P
| Crystal structure of MHC CLass I HLA-A2.1 bound to a photocleavable peptide | Descriptor: | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, BETA-2-MICROGLOBULIN, GLYCEROL, ... | Authors: | Celie, P.H.N, Toebes, M, Rodenko, B, Ovaa, H, Perrakis, A, Schumacher, T.N.M. | Deposit date: | 2010-02-02 | Release date: | 2010-03-02 | Last modified: | 2023-12-20 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Class I Major Histocompatibility Complexes Loaded by a Periodate Trigger. J.Am.Chem.Soc., 131, 2009
|
|
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
|
|
4BOS
| Structure of OTUD2 OTU domain in complex with Ubiquitin K11-linked peptide | Descriptor: | MAGNESIUM ION, NITRATE ION, OTUD2, ... | Authors: | Mevissen, T.E.T, Hospenthal, M.K, Geurink, P.P, Elliott, P.R, Akutsu, M, Arnaudo, N, Ekkebus, R, Kulathu, Y, Wauer, T, El Oualid, F, Freund, S.M.V, Ovaa, H, Komander, D. | Deposit date: | 2013-05-22 | Release date: | 2013-07-24 | Last modified: | 2023-12-20 | Method: | X-RAY DIFFRACTION (2.35 Å) | Cite: | Otu Deubiquitinases Reveal Mechanisms of Linkage Specificity and Enable Ubiquitin Chain Restriction Analysis. Cell(Cambridge,Mass.), 154, 2013
|
|
4BOP
| Structure of OTUD1 OTU domain | Descriptor: | OTU DOMAIN-CONTAINING PROTEIN 1, PHOSPHATE ION | Authors: | Mevissen, T.E.T, Hospenthal, M.K, Geurink, P.P, Elliott, P.R, Akutsu, M, Arnaudo, N, Ekkebus, R, Kulathu, Y, Wauer, T, El Oualid, F, Freund, S.M.V, Ovaa, H, Komander, D. | Deposit date: | 2013-05-22 | Release date: | 2013-07-17 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Otu Deubiquitinases Reveal Mechanisms of Linkage Specificity and Enable Ubiquitin Chain Restriction Analysis. Cell(Cambridge,Mass.), 154, 2013
|
|
4BOU
| Structure of OTUD3 OTU domain | Descriptor: | OTU DOMAIN-CONTAINING PROTEIN 3 | Authors: | Mevissen, T.E.T, Hospenthal, M.K, Geurink, P.P, Elliott, P.R, Akutsu, M, Arnaudo, N, Ekkebus, R, Kulathu, Y, Wauer, T, El Oualid, F, Freund, S.M.V, Ovaa, H, Komander, D. | Deposit date: | 2013-05-22 | Release date: | 2013-07-17 | Last modified: | 2023-12-20 | Method: | X-RAY DIFFRACTION (1.55 Å) | Cite: | Otu Deubiquitinases Reveal Mechanisms of Linkage Specificity and Enable Ubiquitin Chain Restriction Analysis. Cell(Cambridge,Mass.), 154, 2013
|
|
4BOQ
| Structure of OTUD2 OTU domain | Descriptor: | GLYCEROL, UBIQUITIN THIOESTERASE OTU1 | Authors: | Mevissen, T.E.T, Hospenthal, M.K, Geurink, P.P, Elliott, P.R, Akutsu, M, Arnaudo, N, Ekkebus, R, Kulathu, Y, Wauer, T, El Oualid, F, Freund, S.M.V, Ovaa, H, Komander, D. | Deposit date: | 2013-05-22 | Release date: | 2013-07-17 | Last modified: | 2023-12-20 | Method: | X-RAY DIFFRACTION (1.47 Å) | Cite: | Otu Deubiquitinases Reveal Mechanisms of Linkage Specificity and Enable Ubiquitin Chain Restriction Analysis. Cell(Cambridge,Mass.), 154, 2013
|
|
4BOZ
| Structure of OTUD2 OTU domain in complex with K11-linked di ubiquitin | Descriptor: | GLYCEROL, UBIQUITIN THIOESTERASE OTU1, UBIQUITIN-C | Authors: | Mevissen, T.E.T, Hospenthal, M.K, Geurink, P.P, Elliott, P.R, Akutsu, M, Arnaudo, N, Ekkebus, R, Kulathu, Y, Wauer, T, El Oualid, F, Freund, S.M.V, Ovaa, H, Komander, D. | Deposit date: | 2013-05-22 | Release date: | 2013-07-17 | Last modified: | 2023-12-20 | Method: | X-RAY DIFFRACTION (3.03 Å) | Cite: | Otu Deubiquitinases Reveal Mechanisms of Linkage Specificity and Enable Ubiquitin Chain Restriction Analysis. Cell(Cambridge,Mass.), 154, 2013
|
|
6QBS
| The Alkyne Moiety as a Latent Electrophile in Irreversible Covalent Small Molecule Inhibitors of Cathepsin K | Descriptor: | (2~{S})-4-methyl-~{N}-prop-2-enyl-2-[[(1~{S})-2,2,2-tris(fluoranyl)-1-[4-(4-methylsulfonylphenyl)phenyl]ethyl]amino]pentanamide, CALCIUM ION, CHLORIDE ION, ... | Authors: | Mons, E, Jansen, I.D.C, Loboda, J, van Doodewaerd, B.R, Verdoes, M, van Boeckel, C.A.A, van Veelen, P.A, Turk, B, Turk, D, Hermans, J, Ovaa, H. | Deposit date: | 2018-12-21 | Release date: | 2019-02-06 | Last modified: | 2024-01-24 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | The Alkyne Moiety as a Latent Electrophile in Irreversible Covalent Small Molecule Inhibitors of Cathepsin K. J. Am. Chem. Soc., 141, 2019
|
|
6RRH
| GOLGI ALPHA-MANNOSIDASE II | Descriptor: | 1,2-ETHANEDIOL, Alpha-mannosidase 2, ZINC ION | Authors: | Armstrong, Z, Lahav, D, Johnson, R, Kuo, C.L, Beenakker, T.J.M, de Boer, C, Wong, C.S, van Rijssel, E.R, Debets, M, Geurink, P.P, Ovaa, H, van der Stelt, M, Codee, J.D.C, Aerts, J.M.F.G, Wu, L, Overkleeft, H.S, Davies, G.J. | Deposit date: | 2019-05-18 | Release date: | 2020-07-08 | Last modified: | 2024-01-24 | Method: | X-RAY DIFFRACTION (2.07 Å) | Cite: | Manno- epi -cyclophellitols Enable Activity-Based Protein Profiling of Human alpha-Mannosidases and Discovery of New Golgi Mannosidase II Inhibitors. J.Am.Chem.Soc., 142, 2020
|
|
6RRW
| GOLGI ALPHA-MANNOSIDASE II in complex with (2R,3R,4R,5S)-1-(5-{[4-(3,4-Dihydro-2H-1,5-benzodioxepin-7-yl)benzyl]oxy}pentyl)-2-(hydroxymethyl)-3,4,5-piperidinetriol | Descriptor: | (2~{R},3~{R},4~{R},5~{S})-1-[5-[[4-(3,4-dihydro-2~{H}-1,5-benzodioxepin-7-yl)phenyl]methoxy]pentyl]-2-(hydroxymethyl)piperidine-3,4,5-triol, Alpha-mannosidase 2, ZINC ION | Authors: | Armstrong, Z, Lahav, D, Johnson, R, Kuo, C.L, Beenakker, T.J.M, de Boer, C, Wong, C.S, van Rijssel, E.R, Debets, M, Geurink, P.P, Ovaa, H, van der Stelt, M, Codee, J.D.C, Aerts, J.M.F.G, Wu, L, Overkleeft, H.S, Davies, G.J. | Deposit date: | 2019-05-20 | Release date: | 2020-07-08 | Last modified: | 2024-01-24 | Method: | X-RAY DIFFRACTION (2.15 Å) | Cite: | Manno- epi -cyclophellitols Enable Activity-Based Protein Profiling of Human alpha-Mannosidases and Discovery of New Golgi Mannosidase II Inhibitors. J.Am.Chem.Soc., 142, 2020
|
|
6RRN
| GOLGI ALPHA-MANNOSIDASE II in complex with pentyl 2,5-dideoxy-2,5-imino-D-talo-hexonamide | Descriptor: | (2~{S},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)-~{N}-pentyl-pyrrolidine-2-carboxamide, 1,2-ETHANEDIOL, Alpha-mannosidase 2, ... | Authors: | Armstrong, Z, Lahav, D, Johnson, R, Kuo, C.L, Beenakker, T.J.M, de Boer, C, Wong, C.S, van Rijssel, E.R, Debets, M, Geurink, P.P, Ovaa, H, van der Stelt, M, Codee, J.D.C, Aerts, J.M.F.G, Wu, L, Overkleeft, H.S, Davies, G.J. | Deposit date: | 2019-05-20 | Release date: | 2020-07-08 | Last modified: | 2024-01-24 | Method: | X-RAY DIFFRACTION (1.59 Å) | Cite: | Manno- epi -cyclophellitols Enable Activity-Based Protein Profiling of Human alpha-Mannosidases and Discovery of New Golgi Mannosidase II Inhibitors. J.Am.Chem.Soc., 142, 2020
|
|
6RRY
| GOLGI ALPHA-MANNOSIDASE II in complex with (2S,3R)-2-(Hydroxymethyl)-1,2,3,6-tetrahydro-3-pyridinol | Descriptor: | (2~{S},3~{R})-2-(hydroxymethyl)-1,2,3,6-tetrahydropyridin-3-ol, 1,2-ETHANEDIOL, Alpha-mannosidase 2, ... | Authors: | Armstrong, Z, Lahav, D, Johnson, R, Kuo, C.L, Beenakker, T.J.M, de Boer, C, Wong, C.S, van Rijssel, E.R, Debets, M, Geurink, P.P, Ovaa, H, van der Stelt, M, Codee, J.D.C, Aerts, J.M.F.G, Wu, L, Overkleeft, H.S, Davies, G.J. | Deposit date: | 2019-05-20 | Release date: | 2020-07-08 | Last modified: | 2024-01-24 | Method: | X-RAY DIFFRACTION (1.86 Å) | Cite: | Manno- epi -cyclophellitols Enable Activity-Based Protein Profiling of Human alpha-Mannosidases and Discovery of New Golgi Mannosidase II Inhibitors. J.Am.Chem.Soc., 142, 2020
|
|