4E0Y
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![BU of 4e0y by Molmil](/molmil-images/mine/4e0y) | Protelomerase tela covalently complexed with mutated substrate DNA | Descriptor: | DNA (5'-D(*CP*AP*TP*AP*AP*TP*AP*AP*CP*AP*AP*TP*AP*T)-3'), DNA (5'-D(*CP*CP*AP*TP*GP*AP*TP*AP*TP*TP*GP*TP*TP*AP*TP*TP*AP*TP*G)-3'), GLYCEROL, ... | Authors: | Shi, K, Aihara, H. | Deposit date: | 2012-03-05 | Release date: | 2013-02-13 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | An enzyme-catalyzed multistep DNA refolding mechanism in hairpin telomere formation. Plos Biol., 11, 2013
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4DWP
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![BU of 4dwp by Molmil](/molmil-images/mine/4dwp) | SeMet protelomerase tela covalently complexed with substrate DNA | Descriptor: | DNA (5'-D(*CP*AP*TP*GP*AP*TP*AP*TP*TP*GP*TP*TP*AP*TP*TP*GP*TP*AP*A)-3'), DNA (5'-D(*TP*TP*AP*CP*AP*AP*TP*AP*AP*CP*AP*AP*TP*AP*T)-3'), Protelomerase, ... | Authors: | Shi, K, Aihara, H. | Deposit date: | 2012-02-26 | Release date: | 2013-02-13 | Method: | X-RAY DIFFRACTION (2.35 Å) | Cite: | An enzyme-catalyzed multistep DNA refolding mechanism in hairpin telomere formation. Plos Biol., 11, 2013
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4EP4
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![BU of 4ep4 by Molmil](/molmil-images/mine/4ep4) | Thermus thermophilus RuvC structure | Descriptor: | Crossover junction endodeoxyribonuclease RuvC, GLYCEROL, MAGNESIUM ION | Authors: | Chen, L, Shi, K, Yin, Z.Q, Aihara, H. | Deposit date: | 2012-04-17 | Release date: | 2012-11-14 | Last modified: | 2024-02-28 | Method: | X-RAY DIFFRACTION (1.28 Å) | Cite: | Structural asymmetry in the Thermus thermophilus RuvC dimer suggests a basis for sequential strand cleavages during Holliday junction resolution. Nucleic Acids Res., 41, 2013
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7JT4
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![BU of 7jt4 by Molmil](/molmil-images/mine/7jt4) | Crystal Structure of BPTF bromodomain labelled with 5-fluoro-tryptophan | Descriptor: | Nucleosome-remodeling factor subunit BPTF | Authors: | Johnson, J.A, Shi, K, Aihara, H, Pomerantz, W.C.K. | Deposit date: | 2020-08-17 | Release date: | 2021-07-28 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (2.06 Å) | Cite: | Selectivity, ligand deconstruction, and cellular activity analysis of a BPTF bromodomain inhibitor Org.Biomol.Chem., 17, 2019
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4EP5
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![BU of 4ep5 by Molmil](/molmil-images/mine/4ep5) | Thermus thermophilus RuvC structure | Descriptor: | Crossover junction endodeoxyribonuclease RuvC, GLYCEROL, SULFATE ION | Authors: | Chen, L, Shi, K, Yin, Z.Q, Aihara, H. | Deposit date: | 2012-04-17 | Release date: | 2012-11-14 | Last modified: | 2024-02-28 | Method: | X-RAY DIFFRACTION (2.08 Å) | Cite: | Structural asymmetry in the Thermus thermophilus RuvC dimer suggests a basis for sequential strand cleavages during Holliday junction resolution. Nucleic Acids Res., 41, 2013
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4F1I
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![BU of 4f1i by Molmil](/molmil-images/mine/4f1i) | |
4F1H
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![BU of 4f1h by Molmil](/molmil-images/mine/4f1h) | Crystal structure of TDP2 from Danio rerio complexed with a single strand DNA | Descriptor: | DNA (5'-D(P*TP*GP*CP*AP*G)-3'), GLYCEROL, MAGNESIUM ION, ... | Authors: | Shi, K, Kurahashi, K, Aihara, H. | Deposit date: | 2012-05-06 | Release date: | 2012-10-31 | Last modified: | 2024-02-28 | Method: | X-RAY DIFFRACTION (1.662 Å) | Cite: | Structural basis for recognition of 5'-phosphotyrosine adducts by Tdp2. Nat.Struct.Mol.Biol., 19, 2012
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7K33
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![BU of 7k33 by Molmil](/molmil-images/mine/7k33) | Crystal structure of Endonuclease Q complex with 27-mer duplex substrate with an abasic lesion at the active site | Descriptor: | DNA (27-MER), Endonuclease Q, MAGNESIUM ION, ... | Authors: | Shi, K, Moeller, N.M, Banerjee, S, Yin, L, Orellana, K, Aihara, H. | Deposit date: | 2020-09-10 | Release date: | 2021-03-17 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (3.11 Å) | Cite: | Structural basis for recognition of distinct deaminated DNA lesions by endonuclease Q. Proc.Natl.Acad.Sci.USA, 118, 2021
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7K30
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![BU of 7k30 by Molmil](/molmil-images/mine/7k30) | Crystal structure of Endonuclease Q complex with 27-mer duplex substrate with dU at the active site | Descriptor: | 1,2-ETHANEDIOL, DNA (27-MER), Endonuclease Q, ... | Authors: | Shi, K, Moeller, N.M, Banerjee, S, Yin, L, Orellana, K, Aihara, H. | Deposit date: | 2020-09-10 | Release date: | 2021-03-17 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (2.34 Å) | Cite: | Structural basis for recognition of distinct deaminated DNA lesions by endonuclease Q. Proc.Natl.Acad.Sci.USA, 118, 2021
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7K32
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![BU of 7k32 by Molmil](/molmil-images/mine/7k32) | Crystal structure of Endonuclease Q complex with 27-mer duplex substrate with an abasic lesion at the active site | Descriptor: | DNA (27-MER), Endonuclease Q, MAGNESIUM ION, ... | Authors: | Shi, K, Moeller, N.M, Banerjee, S, Yin, L, Orellana, K, Aihara, H. | Deposit date: | 2020-09-10 | Release date: | 2021-03-17 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (3.11 Å) | Cite: | Structural basis for recognition of distinct deaminated DNA lesions by endonuclease Q. Proc.Natl.Acad.Sci.USA, 118, 2021
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7JN3
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![BU of 7jn3 by Molmil](/molmil-images/mine/7jn3) | Cryo-EM structure of Rous sarcoma virus cleaved synaptic complex (CSC) with HIV-1 integrase strand transfer inhibitor MK-2048 | Descriptor: | (6S)-2-(3-chloro-4-fluorobenzyl)-8-ethyl-10-hydroxy-N,6-dimethyl-1,9-dioxo-1,2,6,7,8,9-hexahydropyrazino[1',2':1,5]pyrrolo[2,3-d]pyridazine-4-carboxamide, DNA (5'-D(*AP*AP*TP*GP*TP*TP*GP*TP*CP*TP*TP*AP*TP*GP*CP*AP*AP*T)-3'), DNA (5'-D(*AP*TP*TP*GP*CP*AP*TP*AP*AP*GP*AP*CP*AP*AP*CP*A)-3'), ... | Authors: | Pandey, K.K, Bera, S, Shi, K, Aihara, H, Grandgenett, D.P. | Deposit date: | 2020-08-03 | Release date: | 2021-03-17 | Last modified: | 2024-05-15 | Method: | ELECTRON MICROSCOPY (3.21 Å) | Cite: | Cryo-EM structure of the Rous sarcoma virus octameric cleaved synaptic complex intasome. Commun Biol, 4, 2021
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7K31
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![BU of 7k31 by Molmil](/molmil-images/mine/7k31) | Crystal structure of Endonuclease Q complex with 27-mer duplex substrate with dI at the active site | Descriptor: | 1,2-ETHANEDIOL, CHLORIDE ION, DNA (27-MER), ... | Authors: | Shi, K, Moeller, N.M, Banerjee, S, Yin, L, Orellana, K, Aihara, H. | Deposit date: | 2020-09-10 | Release date: | 2021-03-17 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (2.88 Å) | Cite: | Structural basis for recognition of distinct deaminated DNA lesions by endonuclease Q. Proc.Natl.Acad.Sci.USA, 118, 2021
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7KM5
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![BU of 7km5 by Molmil](/molmil-images/mine/7km5) | Crystal structure of SARS-CoV-2 RBD complexed with Nanosota-1 | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, Spike protein S1, ... | Authors: | Ye, G, Shi, K, Aihara, H, Li, F. | Deposit date: | 2020-11-02 | Release date: | 2021-08-04 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (3.19 Å) | Cite: | The development of Nanosota - 1 as anti-SARS-CoV-2 nanobody drug candidates. Elife, 10, 2021
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7KUI
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![BU of 7kui by Molmil](/molmil-images/mine/7kui) | Cryo-EM structure of Rous sarcoma virus cleaved synaptic complex (CSC) with HIV-1 integrase strand transfer inhibitor MK-2048. CIC region of a cluster identified by 3-dimensional variability analysis in cryoSPARC. | Descriptor: | (6S)-2-(3-chloro-4-fluorobenzyl)-8-ethyl-10-hydroxy-N,6-dimethyl-1,9-dioxo-1,2,6,7,8,9-hexahydropyrazino[1',2':1,5]pyrrolo[2,3-d]pyridazine-4-carboxamide, DNA (5'-D(*AP*AP*TP*GP*TP*TP*GP*TP*CP*TP*TP*AP*TP*GP*CP*AP*AP*T)-3'), DNA (5'-D(*AP*TP*TP*GP*CP*AP*TP*AP*AP*GP*AP*CP*AP*AP*CP*A)-3'), ... | Authors: | Pandey, K.K, Bera, S, Shi, K, Aihara, H, Grandgenett, D.P. | Deposit date: | 2020-11-25 | Release date: | 2021-03-17 | Last modified: | 2024-03-06 | Method: | ELECTRON MICROSCOPY (3.4 Å) | Cite: | Cryo-EM structure of the Rous sarcoma virus octameric cleaved synaptic complex intasome. Commun Biol, 4, 2021
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7KU7
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![BU of 7ku7 by Molmil](/molmil-images/mine/7ku7) | Cryo-EM structure of Rous sarcoma virus cleaved synaptic complex (CSC) with HIV-1 integrase strand transfer inhibitor MK-2048. Cluster identified by 3-dimensional variability analysis in cryoSPARC. | Descriptor: | (6S)-2-(3-chloro-4-fluorobenzyl)-8-ethyl-10-hydroxy-N,6-dimethyl-1,9-dioxo-1,2,6,7,8,9-hexahydropyrazino[1',2':1,5]pyrrolo[2,3-d]pyridazine-4-carboxamide, DNA (5'-D(*AP*AP*TP*GP*TP*TP*GP*TP*CP*TP*TP*AP*TP*GP*CP*AP*AP*T)-3'), DNA (5'-D(*AP*TP*TP*GP*CP*AP*TP*AP*AP*GP*AP*CP*AP*AP*CP*A)-3'), ... | Authors: | Pandey, K.K, Bera, S, Shi, K, Aihara, H, Grandgenett, D.P. | Deposit date: | 2020-11-24 | Release date: | 2021-03-17 | Last modified: | 2024-03-06 | Method: | ELECTRON MICROSCOPY (3.4 Å) | Cite: | Cryo-EM structure of the Rous sarcoma virus octameric cleaved synaptic complex intasome. Commun Biol, 4, 2021
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7M8R
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![BU of 7m8r by Molmil](/molmil-images/mine/7m8r) | Complex structure of Methane monooxygenase hydroxylase and regulatory subunit with fluorosubstituted tryptophans | Descriptor: | 1,1,1-tris(fluoranyl)propan-2-one, 1,2-ETHANEDIOL, BENZOIC ACID, ... | Authors: | Johns, J.C, Banerjee, R, Shi, K, Semonis, M.M, Aihara, H, Pomerantz, W.C.K, Lipscomb, J.D. | Deposit date: | 2021-03-30 | Release date: | 2021-07-28 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (2.22 Å) | Cite: | Soluble Methane Monooxygenase Component Interactions Monitored by 19 F NMR. Biochemistry, 60, 2021
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7M8Q
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![BU of 7m8q by Molmil](/molmil-images/mine/7m8q) | Complex structure of Methane monooxygenase hydroxylase and regulatory subunit with fluorosubstituted tryptophans | Descriptor: | 1,2-ETHANEDIOL, BENZOIC ACID, FE (III) ION, ... | Authors: | Johns, J.C, Banerjee, R, Shi, K, Semonis, M.M, Aihara, H, Pomerantz, W.C.K, Lipscomb, J.D. | Deposit date: | 2021-03-30 | Release date: | 2021-07-28 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (2.08 Å) | Cite: | Soluble Methane Monooxygenase Component Interactions Monitored by 19 F NMR. Biochemistry, 60, 2021
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7M2E
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![BU of 7m2e by Molmil](/molmil-images/mine/7m2e) | Crystal structure of BPTF bromodomain in complex with CB02-092 | Descriptor: | 4-chloro-5-{4-[2-(dimethylamino)ethyl]anilino}-2-methylpyridazin-3(2H)-one, Nucleosome-remodeling factor subunit BPTF | Authors: | Nithianantham, S, Fischer, M. | Deposit date: | 2021-03-16 | Release date: | 2022-02-16 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (1.75 Å) | Cite: | New Design Rules for Developing Potent Cell-Active Inhibitors of the Nucleosome Remodeling Factor (NURF) via BPTF Bromodomain Inhibition J.Med.Chem., 64, 2021
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8FZC
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![BU of 8fzc by Molmil](/molmil-images/mine/8fzc) | |
2NBU
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![BU of 2nbu by Molmil](/molmil-images/mine/2nbu) | |
6Q1M
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![BU of 6q1m by Molmil](/molmil-images/mine/6q1m) | Crystal structure of the wheat dwarf virus Rep domain | Descriptor: | GLYCEROL, Replication-associated protein | Authors: | Litzau, L.A, Everett, B.A, Evans III, R.L, Shi, K, Tompkins, K, Gordon, W.R. | Deposit date: | 2019-08-05 | Release date: | 2019-12-11 | Last modified: | 2023-10-11 | Method: | X-RAY DIFFRACTION (1.24 Å) | Cite: | Crystal structure of the Wheat dwarf virus Rep domain. Acta Crystallogr.,Sect.F, 75, 2019
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2NBW
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![BU of 2nbw by Molmil](/molmil-images/mine/2nbw) | Solution structure of the Rpn1 T1 site with the Rad23 UBL domain | Descriptor: | 26S proteasome regulatory subunit RPN1, UV excision repair protein RAD23 | Authors: | Chen, X, Walters, K.J. | Deposit date: | 2016-03-14 | Release date: | 2016-07-20 | Last modified: | 2024-05-01 | Method: | SOLUTION NMR | Cite: | Structures of Rpn1 T1:Rad23 and hRpn13:hPLIC2 Reveal Distinct Binding Mechanisms between Substrate Receptors and Shuttle Factors of the Proteasome. Structure, 24, 2016
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2NBV
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![BU of 2nbv by Molmil](/molmil-images/mine/2nbv) | |
6CA4
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![BU of 6ca4 by Molmil](/molmil-images/mine/6ca4) | Crystal structure of humanized D. rerio TDP2 by 14 mutations | Descriptor: | 1,2-ETHANEDIOL, MAGNESIUM ION, MALONATE ION, ... | Authors: | Shi, K, Aihrara, H. | Deposit date: | 2018-01-29 | Release date: | 2018-05-02 | Last modified: | 2023-10-04 | Method: | X-RAY DIFFRACTION (1.623 Å) | Cite: | New fluorescence-based high-throughput screening assay for small molecule inhibitors of tyrosyl-DNA phosphodiesterase 2 (TDP2). Eur J Pharm Sci, 118, 2018
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6WDZ
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![BU of 6wdz by Molmil](/molmil-images/mine/6wdz) | Porcine circovirus 2 Rep domain complexed with a single-stranded DNA 10-mer comprising the cleavage site | Descriptor: | 1,2-ETHANEDIOL, ATP-dependent helicase Rep, DNA (5'-D(*TP*AP*GP*TP*AP*TP*TP*AP*CP*C)-3'), ... | Authors: | Litzau, L.A, Tompkins, K, Shi, K, Nelson, A, Evans III, R.L, Gordon, W.R. | Deposit date: | 2020-04-01 | Release date: | 2020-12-16 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (2.03 Å) | Cite: | Molecular underpinnings of ssDNA specificity by Rep HUH-endonucleases and implications for HUH-tag multiplexing and engineering. Nucleic Acids Res., 49, 2021
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