4NQ3
 
 | | Crystal structure of cyanuic acid hydrolase from A. caulinodans | | Descriptor: | BARBITURIC ACID, Cyanuric acid amidohydrolase, MAGNESIUM ION, ... | | Authors: | Cho, S, Shi, K, Aihara, H. | | Deposit date: | 2013-11-23 | | Release date: | 2014-09-10 | | Method: | X-RAY DIFFRACTION (2.702 Å) | | Cite: | Cyanuric acid hydrolase from Azorhizobium caulinodans ORS 571: crystal structure and insights into a new class of Ser-Lys dyad proteins.
Plos One, 9, 2014
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4PT6
 | | The discobody: an engineered discoidin domain from factor VIII that binds v 3 integrin with antibody-like affinities | | Descriptor: | Coagulation factor VIII | | Authors: | Kym, G, Shi, K, Kamajaya, A, Hamdouche, S, Kostecki, J.S, Wannier, T, Li, B, Nikolovski, P, Mayo, S.L. | | Deposit date: | 2014-03-10 | | Release date: | 2015-04-08 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | The discobody: an engineered discoidin domain from factor VIII that binds v 3 integrin with antibody-like affinities
To be Published
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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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5W8N
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5W8X
 | | Lipid A Disaccharide Synthase (LpxB)-7 solubilizing mutations-Bound to UDP | | Descriptor: | Lipid-A-disaccharide synthase, URIDINE-5'-DIPHOSPHATE | | Authors: | Bohl, T.E, Aihara, H, Shi, K, Lee, J.K. | | Deposit date: | 2017-06-22 | | Release date: | 2018-01-31 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.98 Å) | | Cite: | Crystal structure of lipid A disaccharide synthase LpxB from Escherichia coli.
Nat Commun, 9, 2018
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5W8S
 | | Lipid A Disaccharide Synthase (LpxB)-7 solubilizing mutations | | Descriptor: | LITHIUM ION, Lipid-A-disaccharide synthase, SODIUM ION | | Authors: | Bohl, T.E, Aihara, H, Shi, K, Lee, J.K. | | Deposit date: | 2017-06-22 | | Release date: | 2018-01-31 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Crystal structure of lipid A disaccharide synthase LpxB from Escherichia coli.
Nat Commun, 9, 2018
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6B0B
 | | Crystal structure of human APOBEC3H | | Descriptor: | APOBEC3H, MCherry, RNA (5'-R(*UP*AP*AP*AP*AP*AP*AP*A)-3'), ... | | Authors: | Shaban, N.M, Shi, K, Banerjee, S, Harris, R.S, Aihara, H. | | Deposit date: | 2017-09-14 | | Release date: | 2017-10-25 | | Last modified: | 2019-12-04 | | Method: | X-RAY DIFFRACTION (3.2800622 Å) | | Cite: | The Antiviral and Cancer Genomic DNA Deaminase APOBEC3H Is Regulated by an RNA-Mediated Dimerization Mechanism.
Mol. Cell, 69, 2018
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6BBO
 | | Crystal structure of human APOBEC3H/RNA complex | | Descriptor: | APOBEC3H, GLYCEROL, MCherry fluorescent protein, ... | | Authors: | Shaban, N.M, Shi, K, Banerjee, S, Harris, R.S, Aihara, H. | | Deposit date: | 2017-10-19 | | Release date: | 2018-01-10 | | Last modified: | 2023-10-04 | | Method: | X-RAY DIFFRACTION (3.428 Å) | | Cite: | The Antiviral and Cancer Genomic DNA Deaminase APOBEC3H Is Regulated by an RNA-Mediated Dimerization Mechanism.
Mol. Cell, 69, 2018
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6CH1
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6CH3
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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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7KM6
 | | APOBEC3B antibody 5G7 Fv-clasp | | Descriptor: | 1,2-ETHANEDIOL, 5G7 human monoclonal FAB heavy chain, 5G7 human monoclonal FAB light chain, ... | | Authors: | Tang, H, Shi, K, Aihara, H. | | Deposit date: | 2020-11-02 | | Release date: | 2021-05-12 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (1.67 Å) | | Cite: | Structural Characterization of a Minimal Antibody against Human APOBEC3B.
Viruses, 13, 2021
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7MC6
 | | Crystal structure of the SARS-CoV-2 ExoN-nsp10 complex containing Mg2+ ion | | Descriptor: | 1,2-ETHANEDIOL, CHLORIDE ION, MAGNESIUM ION, ... | | Authors: | Moeller, N.M, Shi, K, Banerjee, S, Yin, L, Aihara, H. | | Deposit date: | 2021-04-01 | | Release date: | 2021-05-05 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Structure and dynamics of SARS-CoV-2 proofreading exoribonuclease ExoN.
Proc.Natl.Acad.Sci.USA, 119, 2022
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7MC5
 | | Crystal structure of the SARS-CoV-2 ExoN-nsp10 complex | | Descriptor: | 1,2-ETHANEDIOL, CHLORIDE ION, L(+)-TARTARIC ACID, ... | | Authors: | Moeller, N.M, Shi, K, Banerjee, S, Yin, L, Aihara, H. | | Deposit date: | 2021-04-01 | | Release date: | 2021-05-05 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (1.64 Å) | | Cite: | Structure and dynamics of SARS-CoV-2 proofreading exoribonuclease ExoN.
Proc.Natl.Acad.Sci.USA, 119, 2022
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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: | 2021-10-06 | | 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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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
 | | 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
 | | 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
 | | 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
 | | 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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8WOY
 | | Cryo-EM structure of SARS-CoV-2 Omicron BA.4/5 RBD in complex with rabbit ACE2 (local refinement) | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme, Spike protein S1, ... | | Authors: | Li, L.J, Shi, K.Y, Yu, G.H, Gao, G.F. | | Deposit date: | 2023-10-08 | | Release date: | 2023-12-13 | | Last modified: | 2024-02-28 | | Method: | ELECTRON MICROSCOPY (3.14 Å) | | Cite: | Structural basis of increased binding affinities of spikes from SARS-CoV-2 Omicron variants to rabbit and hare ACE2s reveals the expanding host tendency.
Mbio, 15, 2024
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8WOZ
 | | Cryo-EM structure of SARS-CoV RBD in complex with rabbit ACE2 | | Descriptor: | Angiotensin-converting enzyme, Spike protein S1, ZINC ION | | Authors: | Li, L.J, Shi, K.Y, Yu, G.H, Gao, G.F. | | Deposit date: | 2023-10-08 | | Release date: | 2023-12-13 | | Last modified: | 2024-02-28 | | Method: | ELECTRON MICROSCOPY (3.25 Å) | | Cite: | Structural basis of increased binding affinities of spikes from SARS-CoV-2 Omicron variants to rabbit and hare ACE2s reveals the expanding host tendency.
Mbio, 15, 2024
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8WOX
 | | Cryo-EM structure of SARS-CoV-2 prototype RBD in complex with rabbit ACE2 (local refinement) | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme, Spike protein S1, ... | | Authors: | Li, L.J, Shi, K.Y, Yu, G.H, Gao, G.F. | | Deposit date: | 2023-10-08 | | Release date: | 2023-12-13 | | Last modified: | 2024-02-28 | | Method: | ELECTRON MICROSCOPY (2.75 Å) | | Cite: | Structural basis of increased binding affinities of spikes from SARS-CoV-2 Omicron variants to rabbit and hare ACE2s reveals the expanding host tendency.
Mbio, 15, 2024
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6WE1
 | | Wheat dwarf virus Rep domain complexed with a single-stranded DNA 8-mer comprising the cleavage site | | Descriptor: | DNA (5'-D(*AP*AP*TP*AP*TP*TP*AP*C)-3'), MANGANESE (II) ION, Replication-associated protein | | Authors: | Tompkins, K, Litzau, L.A, Pornschloegl, L, Nelson, A.T, 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 (2.612 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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7LRO
 | | Crystal structure of BPTF bromodomain in complex with inhibitor HZ-01-105 | | Descriptor: | 1,2-ETHANEDIOL, 5-(azetidin-3-ylamino)-4-chloranyl-2-methyl-pyridazin-3-one, DIMETHYL SULFOXIDE, ... | | Authors: | Chan, A, Schonbrunn, E. | | Deposit date: | 2021-02-17 | | Release date: | 2022-08-10 | | Last modified: | 2024-02-21 | | Method: | X-RAY DIFFRACTION (1.45 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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