6S16
| T. thermophilus RuvC in complex with Holliday junction substrate | Descriptor: | CHLORIDE ION, Crossover junction endodeoxyribonuclease RuvC, DNA (33-MER), ... | Authors: | Gorecka, K.M, Krepl, M, Szlachcic, A, Poznanski, J, Sponer, J, Nowotny, M. | Deposit date: | 2019-06-18 | Release date: | 2019-09-25 | Last modified: | 2024-01-24 | Method: | X-RAY DIFFRACTION (3.409 Å) | Cite: | RuvC uses dynamic probing of the Holliday junction to achieve sequence specificity and efficient resolution. Nat Commun, 10, 2019
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6SEH
| Recognition and processing of branched DNA substrates by Slx1-Slx4 nuclease | Descriptor: | Structure-specific endonuclease subunit SLX1, Structure-specific endonuclease subunit SLX4, ZINC ION | Authors: | Gaur, V, Zajko, W, Nirwal, S, Szlachcic, A, Gapinska, M, Nowotny, M. | Deposit date: | 2019-07-30 | Release date: | 2019-09-25 | Last modified: | 2019-12-18 | Method: | X-RAY DIFFRACTION (3.15 Å) | Cite: | Recognition and processing of branched DNA substrates by Slx1-Slx4 nuclease. Nucleic Acids Res., 47, 2019
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6SEI
| Recognition and processing of branched DNA substrates by Slx1-Slx4 nuclease | Descriptor: | CALCIUM ION, DNA (32-MER), Structure-specific endonuclease subunit SLX1, ... | Authors: | Gaur, V, Zajko, W, Nirwal, S, Szlachcic, A, Gapinska, M, Nowotny, M. | Deposit date: | 2019-07-30 | Release date: | 2019-09-25 | Last modified: | 2024-01-24 | Method: | X-RAY DIFFRACTION (2.69 Å) | Cite: | Recognition and processing of branched DNA substrates by Slx1-Slx4 nuclease. Nucleic Acids Res., 47, 2019
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7ZVN
| Crystal structure of human Annexin A2 in complex with full phosphorothioate 5-10 2'-methoxyethyl DNA gapmer antisense oligonucleotide solved at 1.87 A resolution | Descriptor: | 2'-methoxyethyl DNA gapmer antisense oligonucleotide, Annexin A2, CALCIUM ION, ... | Authors: | Hyjek-Skladanowska, M, Anderson, B, Mykhaylyk, V, Orr, C, Wagner, A, Skowronek, K, Seth, P, Nowotny, M. | Deposit date: | 2022-05-16 | Release date: | 2022-09-14 | Last modified: | 2024-02-07 | Method: | X-RAY DIFFRACTION (1.87 Å) | Cite: | Structures of annexin A2-PS DNA complexes show dominance of hydrophobic interactions in phosphorothioate binding. Nucleic Acids Res., 51, 2023
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7ZVX
| Crystal structure of human Annexin A2 in complex with full phosphorothioate 5-10 2'-methoxyethyl DNA gapmer antisense oligonucleotide solved at 2.4 A resolution | Descriptor: | 1,2-ETHANEDIOL, 2'-methoxyethyl DNA gapmer antisense oligonucleotide, Annexin A2, ... | Authors: | Hyjek-Skladanowska, M, Anderson, B, Mykhaylyk, V, Orr, C, Wagner, A, Skowronek, K, Seth, P, Nowotny, M. | Deposit date: | 2022-05-17 | Release date: | 2022-09-14 | Last modified: | 2024-02-07 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Structures of annexin A2-PS DNA complexes show dominance of hydrophobic interactions in phosphorothioate binding. Nucleic Acids Res., 51, 2023
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6YWN
| CutA in complex with CMPCPP | Descriptor: | 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine, CALCIUM ION, CutA | Authors: | Malik, D, Kobylecki, K, Krawczyk, P, Poznanski, J, Jakielaszek, A, Napiorkowska, A, Dziembowski, A, Tomecki, R, Nowotny, M. | Deposit date: | 2020-04-29 | Release date: | 2020-08-05 | Last modified: | 2020-09-30 | Method: | X-RAY DIFFRACTION (1.45 Å) | Cite: | Structure and mechanism of CutA, RNA nucleotidyl transferase with an unusual preference for cytosine. Nucleic Acids Res., 48, 2020
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6YWP
| Structure of apo-CutA | Descriptor: | CutA, MAGNESIUM ION | Authors: | Malik, D, Kobylecki, K, Krawczyk, P, Poznanski, J, Jakielaszek, A, Napiorkowska, A, Dziembowski, A, Tomecki, R, Nowotny, M. | Deposit date: | 2020-04-29 | Release date: | 2020-08-05 | Last modified: | 2020-09-30 | Method: | X-RAY DIFFRACTION (2.25 Å) | Cite: | Structure and mechanism of CutA, RNA nucleotidyl transferase with an unusual preference for cytosine. Nucleic Acids Res., 48, 2020
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6STY
| Human REXO2 exonuclease in complex with RNA. | Descriptor: | CALCIUM ION, Oligoribonuclease, mitochondrial, ... | Authors: | Malik, D, Szewczyk, M, Szczesny, R, Nowotny, M. | Deposit date: | 2019-09-12 | Release date: | 2020-04-29 | Last modified: | 2024-01-24 | Method: | X-RAY DIFFRACTION (3.15 Å) | Cite: | Human REXO2 controls short mitochondrial RNAs generated by mtRNA processing and decay machinery to prevent accumulation of double-stranded RNA. Nucleic Acids Res., 48, 2020
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6GKK
| Translation initiation factor 4E in complex with beta-phosphorothioate trinucleotide mRNA 5' cap diastereomer 1 (m7GppSpApG D1) | Descriptor: | Eukaryotic translation initiation factor 4E, GLYCEROL, [(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-7-ium-9-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methyl [phosphonooxy(sulfanyl)phosphoryl] hydrogen phosphate | Authors: | Warminski, M, Nowak, E, Kowalska, J, Jemielity, J, Nowotny, M. | Deposit date: | 2018-05-21 | Release date: | 2019-06-19 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (1.858 Å) | Cite: | Translation initiation factor 4E in complex with beta-phosphorothioate trinucleotide mRNA 5' cap diastereomer 1 (m7GppSpApG D1) To Be Published
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6GKJ
| Translation initiation factor 4E in complex with trinucleotide mRNA 5' cap (m7GpppApG) | Descriptor: | 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE, Eukaryotic translation initiation factor 4E, GLYCEROL | Authors: | Warminski, M, Nowak, E, Kowalska, J, Jemielity, J, Nowotny, M. | Deposit date: | 2018-05-21 | Release date: | 2019-06-19 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (2.068 Å) | Cite: | Translation initiation factor 4E in complex with trinucleotide mRNA 5' cap (m7GpppApG) To Be Published
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6GKL
| Translation initiation factor 4E in complex with beta-phosphorothioate trinucleotide mRNA 5' cap diastereomer 2 (m7GppSpApG D2) | Descriptor: | Eukaryotic translation initiation factor 4E, GLYCEROL, [[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-4,5-dihydropurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-sulfanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate | Authors: | Warminski, M, Nowak, E, Kowalska, J, Jemielity, J, Nowotny, M. | Deposit date: | 2018-05-21 | Release date: | 2019-06-19 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Translation initiation factor 4E in complex with beta-phosphorothioate trinucleotide mRNA 5' cap diastereomer 2 (m7GppSpApG D2) To Be Published
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8R41
| Structure of CHI3L1 in complex with inhibitor 1 | Descriptor: | 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, BROMIDE ION, ... | Authors: | Nowak, E, Napiorkowska-Gromadzka, A, Nowotny, M. | Deposit date: | 2023-11-10 | Release date: | 2024-03-13 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (2.25 Å) | Cite: | Structure-Based Discovery of High-Affinity Small Molecule Ligands and Development of Tool Probes to Study the Role of Chitinase-3-Like Protein 1. J.Med.Chem., 67, 2024
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8R4X
| Structure of Chitinase-3-like protein 1 in complex with inhibitor 30 | Descriptor: | (2~{S},5~{S})-4-[1-(4-chloranylpyridin-2-yl)piperidin-4-yl]-5-[(4-chlorophenyl)methyl]-2-methyl-morpholine, 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... | Authors: | Nowak, E, Napiorkowska-Gromadzka, A, Nowotny, M. | Deposit date: | 2023-11-14 | Release date: | 2024-03-13 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (1.54 Å) | Cite: | Structure-Based Discovery of High-Affinity Small Molecule Ligands and Development of Tool Probes to Study the Role of Chitinase-3-Like Protein 1. J.Med.Chem., 67, 2024
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3O3F
| T. maritima RNase H2 D107N in complex with nucleic acid substrate and magnesium ions | Descriptor: | DNA (5'-D(*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*C)-3'), DNA/RNA (5'-D(*GP*AP*CP*AP*C)-R(P*C)-D(P*TP*GP*AP*TP*TP*C)-3'), MAGNESIUM ION, ... | Authors: | Rychlik, M.P, Chon, H, Cerritelli, S.M, Klimek, P, Crouch, R.J, Nowotny, M. | Deposit date: | 2010-07-24 | Release date: | 2010-12-08 | Last modified: | 2024-02-21 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Crystal Structures of RNase H2 in Complex with Nucleic Acid Reveal the Mechanism of RNA-DNA Junction Recognition and Cleavage. Mol.Cell, 40, 2010
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3O3H
| T. maritima RNase H2 D107N in complex with nucleic acid substrate and manganese ions | Descriptor: | DNA (5'-D(*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*C)-3'), DNA/RNA (5'-D(*GP*AP*CP*AP*C)-R(P*C)-D(P*TP*GP*AP*TP*TP*C)-3'), MANGANESE (II) ION, ... | Authors: | Rychlik, M.P, Chon, H, Cerritelli, S.M, Klimek, P, Crouch, R.J, Nowotny, M. | Deposit date: | 2010-07-24 | Release date: | 2010-12-08 | Last modified: | 2024-02-21 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Crystal Structures of RNase H2 in Complex with Nucleic Acid Reveal the Mechanism of RNA-DNA Junction Recognition and Cleavage. Mol.Cell, 40, 2010
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3O3G
| T. maritima RNase H2 in complex with nucleic acid substrate and calcium ions | Descriptor: | CALCIUM ION, DNA (5'-D(*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*C)-3'), DNA/RNA (5'-D(*GP*AP*CP*AP*C)-R(P*C)-D(P*TP*GP*AP*TP*TP*C)-3'), ... | Authors: | Rychlik, M.P, Chon, H, Cerritelli, S.M, Klimek, P, Crouch, R.J, Nowotny, M. | Deposit date: | 2010-07-24 | Release date: | 2010-12-08 | Last modified: | 2023-09-06 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Crystal Structures of RNase H2 in Complex with Nucleic Acid Reveal the Mechanism of RNA-DNA Junction Recognition and Cleavage. Mol.Cell, 40, 2010
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4Q0W
| he catalytic core of Rad2 in complex with DNA substrate (complex II) | Descriptor: | CALCIUM ION, DNA (5'-D(*TP*TP*AP*GP*GP*TP*GP*GP*AP*CP*GP*GP*AP*TP*CP*AP*TP*T)-3'), DNA (5'-D(*TP*TP*TP*GP*AP*TP*CP*CP*GP*TP*CP*CP*AP*CP*CP*TP*TP*T)-3'), ... | Authors: | Mietus, M, Nowak, E, Jaciuk, M, Kustosz, P, Nowotny, M. | Deposit date: | 2014-04-02 | Release date: | 2014-08-27 | Last modified: | 2023-09-20 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Crystal structure of the catalytic core of Rad2: insights into the mechanism of substrate binding. Nucleic Acids Res., 42, 2014
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4Q10
| The catalytic core of Rad2 in complex with DNA substrate (complex IV) | Descriptor: | CALCIUM ION, DNA (5'-D(*TP*TP*TP*TP*CP*TP*GP*AP*GP*AP*CP*AP*AP*GP*GP*GP*AP*GP*CP*TP*TP*TP*T)-3'), DNA (5'-D(*TP*TP*TP*TP*GP*CP*TP*CP*CP*CP*TP*TP*GP*TP*CP*TP*CP*AP*GP*TP*TP*TP*T)-3'), ... | Authors: | Mietus, M, Nowak, E, Jaciuk, M, Kustosz, P, Nowotny, M. | Deposit date: | 2014-04-02 | Release date: | 2014-08-27 | Last modified: | 2023-09-20 | Method: | X-RAY DIFFRACTION (2.7 Å) | Cite: | Crystal structure of the catalytic core of Rad2: insights into the mechanism of substrate binding. Nucleic Acids Res., 42, 2014
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4Q0R
| The catalytic core of Rad2 (complex I) | Descriptor: | DNA (5'-D(*CP*TP*GP*AP*GP*TP*CP*AP*GP*AP*GP*CP*AP*AP*A)-3'), DNA repair protein RAD2 | Authors: | Mietus, M, Nowak, E, Jaciuk, M, Kustosz, P, Nowotny, M. | Deposit date: | 2014-04-02 | Release date: | 2014-08-27 | Last modified: | 2017-08-09 | Method: | X-RAY DIFFRACTION (2.75 Å) | Cite: | Crystal structure of the catalytic core of Rad2: insights into the mechanism of substrate binding. Nucleic Acids Res., 42, 2014
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4Q0Z
| The catalytic core of Rad2 in complex with DNA substrate (complex III) | Descriptor: | CALCIUM ION, DNA (5'-D(*TP*CP*TP*GP*AP*GP*AP*CP*AP*AP*GP*GP*GP*AP*GP*CP*T)-3'), DNA (5'-D(*TP*GP*CP*TP*CP*CP*CP*TP*TP*GP*TP*CP*TP*CP*AP*GP*T)-3'), ... | Authors: | Mietus, M, Nowak, E, Jaciuk, M, Kustosz, P, Nowotny, M. | Deposit date: | 2014-04-02 | Release date: | 2014-08-27 | Last modified: | 2023-09-20 | Method: | X-RAY DIFFRACTION (2.398 Å) | Cite: | Crystal structure of the catalytic core of Rad2: insights into the mechanism of substrate binding. Nucleic Acids Res., 42, 2014
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4PY5
| Thermovibrio ammonificans RNase H3 in complex with 19-mer RNA/DNA | Descriptor: | 5'-D(*GP*GP*AP*AP*TP*CP*AP*GP*GP*TP*GP*TP*CP*GP*CP*AP*CP*TP*C)-3', 5'-R(*GP*AP*GP*UP*GP*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP*C)-3', GLYCEROL, ... | Authors: | Figiel, M, Nowotny, M. | Deposit date: | 2014-03-26 | Release date: | 2014-07-30 | Last modified: | 2014-10-29 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Crystal structure of RNase H3-substrate complex reveals parallel evolution of RNA/DNA hybrid recognition. Nucleic Acids Res., 42, 2014
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4LD0
| T. thermophilus RuvC in complex with Holliday junction substrate | Descriptor: | Crossover junction endodeoxyribonuclease RuvC, DNA 11-MER, DNA 13-MER, ... | Authors: | Gorecka, K.M, Komorowska, W, Nowotny, M. | Deposit date: | 2013-06-24 | Release date: | 2013-09-04 | Last modified: | 2024-02-28 | Method: | X-RAY DIFFRACTION (3.75 Å) | Cite: | Crystal structure of RuvC resolvase in complex with Holliday junction substrate. Nucleic Acids Res., 41, 2013
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5M7V
| Translation initiation factor 4E in complex with (RP)-m2(7,2'O)GppSpG mRNA 5' cap analog (beta-S-ARCA D1) | Descriptor: | Eukaryotic translation initiation factor 4E, GLYCEROL, [(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-7-ium-9-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methyl [phosphonooxy(sulfanyl)phosphoryl] hydrogen phosphate | Authors: | Warminski, M, Nowak, E, Kowalska, J, Jemielity, J, Nowotny, M. | Deposit date: | 2016-10-28 | Release date: | 2017-12-20 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (1.74 Å) | Cite: | Translation initiation factor 4E in complex with (RP)-m2(7,2'O)GppSpG mRNA 5' cap analog (beta-S-ARCA D1) To Be Published
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5M84
| Translation initiation factor 4E in complex with (SP)-m2(7,2'O)GppSpA mRNA 5' cap analog | Descriptor: | Eukaryotic translation initiation factor 4E, GLYCEROL, [[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-sulfanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanyl-purin-7-ium-9-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methyl hydrogen phosphate | Authors: | Warminski, M, Nowak, E, Kowalska, J, Jemielity, J, Nowotny, M. | Deposit date: | 2016-10-28 | Release date: | 2017-12-20 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (1.85 Å) | Cite: | Translation initiation factor 4E in complex with (SP)-m2(7,2'O)GppSpA mRNA 5' cap analog To Be Published
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5M7Z
| Translation initiation factor 4E in complex with (SP)-m2(7,2'O)GppSepG mRNA 5' cap analog (beta-Se-ARCA D2) | Descriptor: | CHLORIDE ION, Eukaryotic translation initiation factor 4E, GLYCEROL, ... | Authors: | Warminski, M, Nowak, E, Kowalska, J, Jemielity, J, Nowotny, M. | Deposit date: | 2016-10-28 | Release date: | 2017-12-20 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (1.689 Å) | Cite: | Translation initiation factor 4E in complex with (SP)-m2(7,2'O)GppSepG mRNA 5' cap analog (beta-Se-ARCA D2) To Be Published
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