7ENB
 
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7EMZ
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7EYW
 | | Fe(II)/(alpha)ketoglutarate-dependent dioxygenase SptF with terretonin C | | Descriptor: | 2-oxoglutarate/Fe(II)-dependent dioxygenase SptF, FE (II) ION, N-OXALYLGLYCINE, ... | | Authors: | Tao, H, Mori, T, Abe, I. | | Deposit date: | 2021-06-01 | | Release date: | 2022-04-20 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Molecular insights into the unusually promiscuous and catalytically versatile Fe(II)/ alpha-ketoglutarate-dependent oxygenase SptF.
Nat Commun, 13, 2022
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7EYU
 | | Fe(II)/(alpha)ketoglutarate-dependent dioxygenase SptF-N65T mutant with andiconin D | | Descriptor: | 2-oxoglutarate/Fe(II)-dependent dioxygenase SptF, Andiconin D, FE (II) ION, ... | | Authors: | Tao, H, Mori, T, Abe, I. | | Deposit date: | 2021-06-01 | | Release date: | 2022-04-20 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.05 Å) | | Cite: | Molecular insights into the unusually promiscuous and catalytically versatile Fe(II)/ alpha-ketoglutarate-dependent oxygenase SptF.
Nat Commun, 13, 2022
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7FCB
 | | SptF 9 residues truncated mutant | | Descriptor: | 2-oxoglutarate/Fe(II)-dependent dioxygenase SptF, FE (II) ION, N-OXALYLGLYCINE | | Authors: | Hui, T, Mori, T, Abe, I. | | Deposit date: | 2021-07-14 | | Release date: | 2022-04-20 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.4 Å) | | Cite: | Molecular insights into the unusually promiscuous and catalytically versatile Fe(II)/ alpha-ketoglutarate-dependent oxygenase SptF.
Nat Commun, 13, 2022
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7EYT
 | | Fe(II)/(alpha)ketoglutarate-dependent dioxygenase SptF with andilesin C and NOG | | Descriptor: | 2-oxoglutarate/Fe(II)-dependent dioxygenase SptF, Andilesin C, FE (II) ION, ... | | Authors: | Tao, H, Mori, T, Abe, I. | | Deposit date: | 2021-06-01 | | Release date: | 2022-04-20 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Molecular insights into the unusually promiscuous and catalytically versatile Fe(II)/ alpha-ketoglutarate-dependent oxygenase SptF.
Nat Commun, 13, 2022
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7EUT
 | | Crystal structures of 2-oxoglutarate dependent dioxygenase (CTB9) in complex with N-oxalylglycine | | Descriptor: | 1,2-ETHANEDIOL, 2-oxoglutarate (2-OG)-dependent dioxygenase, COPPER (II) ION, ... | | Authors: | Hou, X.D, Liu, X.Z, Yuan, Z.B, Yin, D.J, Rao, Y.J. | | Deposit date: | 2021-05-18 | | Release date: | 2022-05-25 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.497 Å) | | Cite: | Molecular Basis of the Unusual Seven-Membered Methylenedioxy Bridge Formation Catalyzed by Fe(II)/alpha-KG-Dependent Oxygenase CTB9
Acs Catalysis, 12, 2022
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7EUU
 | | Crystal structures of 2-oxoglutarate dependent dioxygenase (CTB9) in complex with N-oxalylglycine and pre-cercosporin | | Descriptor: | 1,2-ETHANEDIOL, 2,6,11-trimethoxy-4,7,9-tris(oxidanyl)-1,12-bis[(2R)-2-oxidanylpropyl]perylene-3,10-dione, 2-oxoglutarate (2-OG)-dependent dioxygenase, ... | | Authors: | Hou, X.D, Liu, X.Z, Yuan, Z.B, Rao, Y.J. | | Deposit date: | 2021-05-18 | | Release date: | 2022-05-25 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.202 Å) | | Cite: | Molecular Basis of the Unusual Seven-Membered Methylenedioxy Bridge Formation Catalyzed by Fe(II)/alpha-KG-Dependent Oxygenase CTB9
Acs Catalysis, 12, 2022
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7CL5
 | | The crystal structure of KanJ in complex with kanamycin B and N-oxalylglycine | | Descriptor: | (1R,2S,3S,4R,6S)-4,6-DIAMINO-3-[(3-AMINO-3-DEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY]-2-HYDROXYCYCLOHEXYL 2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSIDE, Kanamycin B dioxygenase, N-OXALYLGLYCINE, ... | | Authors: | Kitayama, Y, Miyanaga, A, Kudo, F, Eguchi, T. | | Deposit date: | 2020-07-20 | | Release date: | 2021-01-13 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Stepwise Post-glycosylation Modification of Sugar Moieties in Kanamycin Biosynthesis.
Chembiochem, 22, 2021
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7CL4
 | | The crystal structure of KanJ in complex with N-oxalylglycine | | Descriptor: | Kanamycin B dioxygenase, N-OXALYLGLYCINE, NICKEL (II) ION | | Authors: | Kitayama, Y, Miyanaga, A, Kudo, F, Eguchi, T. | | Deposit date: | 2020-07-20 | | Release date: | 2021-01-13 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.25 Å) | | Cite: | Stepwise Post-glycosylation Modification of Sugar Moieties in Kanamycin Biosynthesis.
Chembiochem, 22, 2021
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7CL6
 | | The crystal structure of KanJ in complex with neamine and N-oxalylglycine | | Descriptor: | (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside, Kanamycin B dioxygenase, N-OXALYLGLYCINE, ... | | Authors: | Kitayama, Y, Miyanaga, A, Kudo, F, Eguchi, T. | | Deposit date: | 2020-07-20 | | Release date: | 2021-01-13 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.44 Å) | | Cite: | Stepwise Post-glycosylation Modification of Sugar Moieties in Kanamycin Biosynthesis.
Chembiochem, 22, 2021
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7Q5V
 | | HIF PROLYL HYDROXYLASE 2 (PHD2/EGLN1) IN COMPLEX WITH N-OXALYLGLYCINE (NOG) AND HIF-2 ALPHA CODD (523-542) | | Descriptor: | CHLORIDE ION, DI(HYDROXYETHYL)ETHER, Egl nine homolog 1, ... | | Authors: | Figg Jr, W.D, McDonough, M.A, Chowdhury, R, Nakashima, Y, Schofield, C.J. | | Deposit date: | 2021-11-04 | | Release date: | 2022-11-16 | | Last modified: | 2024-01-31 | | Method: | X-RAY DIFFRACTION (1.17 Å) | | Cite: | Structural basis for binding of the renal carcinoma target hypoxia-inducible factor 2 alpha to prolyl hydroxylase domain 2.
Proteins, 91, 2023
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6TP5
 | | Crystal structure of human Transmembrane prolyl 4-hydroxylase | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CALCIUM ION, CHLORIDE ION, ... | | Authors: | Myllykoski, M, Sutinen, A, Koski, M.K, Kallio, J.P, Raasakka, A, Myllyharju, J, Wierenga, R.K, Koivunen, P. | | Deposit date: | 2019-12-12 | | Release date: | 2020-12-23 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (2.25 Å) | | Cite: | Structure of transmembrane prolyl 4-hydroxylase reveals unique organization of EF and dioxygenase domains.
J.Biol.Chem., 296, 2020
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7VPN
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7VBQ
 | | Heterodimer structure of Fe(II)/(alpha)ketoglutarate-dependent dioxygenase TlxIJ | | Descriptor: | FE (III) ION, Fe(II)/(alpha)ketoglutarate-dependent dioxygenase TlxI, Fe(II)/(alpha)ketoglutarate-dependent dioxygenase TlxJ, ... | | Authors: | Li, X, Awakawa, T, Mori, T, Abe, I. | | Deposit date: | 2021-09-01 | | Release date: | 2022-04-20 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.95 Å) | | Cite: | Heterodimeric Non-heme Iron Enzymes in Fungal Meroterpenoid Biosynthesis.
J.Am.Chem.Soc., 143, 2021
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7WL0
 | | Crystal structure of human ALKBH5 in complex with N-oxalylglycine (NOG) and m6A-containing ssRNA | | Descriptor: | FORMIC ACID, MANGANESE (II) ION, N-OXALYLGLYCINE, ... | | Authors: | Kaur, S, McDonough, M.A, Schofield, C.J, Aik, W.S. | | Deposit date: | 2022-01-12 | | Release date: | 2022-03-30 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Mechanisms of substrate recognition and N6-methyladenosine demethylation revealed by crystal structures of ALKBH5-RNA complexes.
Nucleic Acids Res., 50, 2022
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7W5P
 | | Crystal Structure of the dioxygenase CcTet from Coprinopsis cinereain bound to 12bp N6-methyldeoxyadenine (6mA) containing duplex DNA | | Descriptor: | CcTet, DNA, DNA (12-MER), ... | | Authors: | Mu, Y.J, Zhang, L, Zhang, L. | | Deposit date: | 2021-11-30 | | Release date: | 2022-03-30 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | A fungal dioxygenase CcTet serves as a eukaryotic 6mA demethylase on duplex DNA.
Nat.Chem.Biol., 18, 2022
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5Y1B
 | | Crystal Structure of insect beta-N-acetyl-D-hexosaminidase OfHex1 complexed with a berberine derivative (SYSU-00679) | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 9-O-3'-quinolinium propylberberine, Beta-hexosaminidase | | Authors: | Duan, Y.W, Liu, T, Zhou, Y, Tang, J.Y, Li, M, Yang, Q. | | Deposit date: | 2017-07-20 | | Release date: | 2018-01-24 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.207 Å) | | Cite: | Glycoside hydrolase family 18 and 20 enzymes are novel targets of the traditional medicine berberine.
J. Biol. Chem., 293, 2018
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5Y0V
 | | Crystal Structure of insect beta-N-acetyl-D-hexosaminidase OfHex1 complexed with berberine | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, BERBERINE, ... | | Authors: | Duan, Y.W, Liu, T, Tang, J.Y, Li, M, Yang, Q. | | Deposit date: | 2017-07-18 | | Release date: | 2018-01-24 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.423 Å) | | Cite: | Glycoside hydrolase family 18 and 20 enzymes are novel targets of the traditional medicine berberine.
J. Biol. Chem., 293, 2018
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8H68
 | | Crystal structure of Caenorhabditis elegans NMAD-1 in complex with NOG and Mg(II) | | Descriptor: | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, DI(HYDROXYETHYL)ETHER, ... | | Authors: | Shi, Y, Ding, J, Yang, H. | | Deposit date: | 2022-10-16 | | Release date: | 2023-02-22 | | Last modified: | 2023-09-20 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Caenorhabditis elegans NMAD-1 functions as a demethylase for actin.
J Mol Cell Biol, 15, 2023
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6BYK
 | | Structure of 14-3-3 beta/alpha bound to O-ClcNAc peptide | | Descriptor: | 14-3-3 protein beta/alpha, 2-acetamido-2-deoxy-beta-D-glucopyranose, ATPPVSQASSTT O-GlcNac peptide | | Authors: | Schumacher, M.A. | | Deposit date: | 2017-12-20 | | Release date: | 2018-05-09 | | Last modified: | 2023-10-04 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Structural basis of O-GlcNAc recognition by mammalian 14-3-3 proteins.
Proc.Natl.Acad.Sci.USA, 115, 2018
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5DIY
 | | Thermobaculum terrenum O-GlcNAc hydrolase mutant - D120N | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, Hyaluronidase, TGF-beta-activated kinase 1 and MAP3K7-binding protein 1 | | Authors: | Ostrowski, A, Gundogdu, M, Ferenbach, A.T, Lebedev, A, van Aalten, D.M.F. | | Deposit date: | 2015-09-01 | | Release date: | 2015-10-28 | | Last modified: | 2020-07-29 | | Method: | X-RAY DIFFRACTION (2.06 Å) | | Cite: | Evidence for a Functional O-Linked N-Acetylglucosamine (O-GlcNAc) System in the Thermophilic Bacterium Thermobaculum terrenum.
J.Biol.Chem., 290, 2015
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5OBM
 | | Crystal structure of Gentamicin bound to the yeast 80S ribosome | | Descriptor: | (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL, 18S ribosomal RNA, 25S ribosomal RNA, ... | | Authors: | Prokhorova, I, Djumagulov, M, Urzhumtsev, A, Yusupov, M, Yusupova, G. | | Deposit date: | 2017-06-28 | | Release date: | 2017-12-13 | | Last modified: | 2024-05-08 | | Method: | X-RAY DIFFRACTION (3.4 Å) | | Cite: | Aminoglycoside interactions and impacts on the eukaryotic ribosome.
Proc. Natl. Acad. Sci. U.S.A., 114, 2017
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5ON6
 | | Crystal structure of haemanthamine bound to the 80S ribosome | | Descriptor: | 18S ribosomal RNA, 25S ribosomal RNA, 40S ribosomal protein S0-A, ... | | Authors: | Pellegrino, S, Meyer, M, Yusupova, G, Yusupov, M. | | Deposit date: | 2017-08-03 | | Release date: | 2018-02-28 | | Last modified: | 2024-05-08 | | Method: | X-RAY DIFFRACTION (3.10000229 Å) | | Cite: | The Amaryllidaceae Alkaloid Haemanthamine Binds the Eukaryotic Ribosome to Repress Cancer Cell Growth.
Structure, 26, 2018
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1EAV
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