5SWW
 
 | | Crystal Structure of Human APOBEC3A complexed with ssDNA | | Descriptor: | DNA 15-Mer, DNA dC->dU-editing enzyme APOBEC-3A, GLYCEROL, ... | | Authors: | Shi, K, Banerjee, S, Kurahashi, K, Aihara, H. | | Deposit date: | 2016-08-09 | | Release date: | 2016-12-28 | | Last modified: | 2023-10-04 | | Method: | X-RAY DIFFRACTION (3.151 Å) | | Cite: | Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B.
Nat. Struct. Mol. Biol., 24, 2017
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5SXG
 | | Crystal Structure of the Cancer Genomic DNA Mutator APOBEC3B | | Descriptor: | 1,3-PROPANDIOL, DNA dC->dU-editing enzyme APOBEC-3B, IMIDAZOLE, ... | | Authors: | Shi, K, Kurahashi, K, Aihara, H. | | Deposit date: | 2016-08-09 | | Release date: | 2017-12-27 | | Last modified: | 2023-10-04 | | Method: | X-RAY DIFFRACTION (1.93 Å) | | Cite: | Conformational Switch Regulates the DNA Cytosine Deaminase Activity of Human APOBEC3B.
Sci Rep, 7, 2017
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5TD5
 | | Crystal Structure of Human APOBEC3B variant complexed with ssDNA | | Descriptor: | 1,2-ETHANEDIOL, CHLORIDE ION, DNA (5'-D(P*TP*TP*CP*AP*T)-3'), ... | | Authors: | Shi, K, Banerjee, S, Kurahashi, K, Aihara, H. | | Deposit date: | 2016-09-16 | | Release date: | 2016-12-28 | | Last modified: | 2024-03-06 | | Method: | X-RAY DIFFRACTION (1.718 Å) | | Cite: | Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B.
Nat. Struct. Mol. Biol., 24, 2017
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5U0L
 | | X-ray crystal structure of fatty aldehyde dehydrogenase enzymes from Marinobacter aquaeolei VT8 complexed with a substrate | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, 1,2-ETHANEDIOL, CHLORIDE ION, ... | | Authors: | Shi, K, Mulliner, K, Barney, B.M, Aihara, H. | | Deposit date: | 2016-11-24 | | Release date: | 2017-04-26 | | Last modified: | 2023-10-04 | | Method: | X-RAY DIFFRACTION (2.285 Å) | | Cite: | Five Fatty Aldehyde Dehydrogenase Enzymes from Marinobacter and Acinetobacter spp. and Structural Insights into the Aldehyde Binding Pocket.
Appl. Environ. Microbiol., 83, 2017
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5U0M
 | | Fatty aldehyde dehydrogenase from Marinobacter aquaeolei VT8 and cofactor complex | | Descriptor: | 1,2-ETHANEDIOL, CITRIC ACID, N-succinylglutamate 5-semialdehyde dehydrogenase, ... | | Authors: | Shi, K, Mulliner, K, Barney, B.M, Aihara, H. | | Deposit date: | 2016-11-24 | | Release date: | 2017-04-26 | | Last modified: | 2023-10-04 | | Method: | X-RAY DIFFRACTION (3.075 Å) | | Cite: | Five Fatty Aldehyde Dehydrogenase Enzymes from Marinobacter and Acinetobacter spp. and Structural Insights into the Aldehyde Binding Pocket.
Appl. Environ. Microbiol., 83, 2017
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6U82
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6U81
 | | Crystal Structure of the Double Homeodomain of DUX4 in Complex with a DNA aptamer | | Descriptor: | 1,2-ETHANEDIOL, DNA (5'-D(*GP*CP*GP*TP*AP*AP*TP*CP*TP*AP*AP*TP*CP*AP*AP*CP*A)-3'), DNA (5'-D(*TP*GP*TP*TP*GP*AP*TP*TP*AP*GP*CP*CP*CP*AP*TP*TP*AP*CP*GP*C)-3'), ... | | Authors: | Shi, K, Aihara, H. | | Deposit date: | 2019-09-04 | | Release date: | 2020-02-19 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (2.34 Å) | | Cite: | DNA aptamers against the DUX4 protein reveal novel therapeutic implications for FSHD.
Faseb J., 34, 2020
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1BMQ
 | | CRYSTAL STRUCTURE OF THE COMPLEX OF INTERLEUKIN-1BETA CONVERTING ENZYME (ICE) WITH A PEPTIDE BASED INHIBITOR, (3S )-N-METHANESULFONYL-3-({1-[N-(2-NAPHTOYL)-L-VALYL]-L-PROLYL }AMINO)-4-OXOBUTANAMIDE | | Descriptor: | (3S)-N-METHANESULFONYL-3-({1-[N-(2-NAPHTOYL)-L-VALYL]-L-PROLYL}AMINO)-4-OXOBUTANAMIDE, PROTEIN (INTERLEUKIN-1 BETA CONVERTASE) | | Authors: | Okamoto, Y, Anan, H, Nakai, E, Morihira, K, Yonetoku, Y, Kurihara, H, Katayama, N, Sakashita, H, Terai, Y, Takeuchi, M, Shibanuma, T, Isomura, Y. | | Deposit date: | 1998-07-24 | | Release date: | 1998-07-29 | | Last modified: | 2023-08-09 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Peptide based interleukin-1 beta converting enzyme (ICE) inhibitors: synthesis, structure activity relationships and crystallographic study of the ICE-inhibitor complex.
Chem.Pharm.Bull., 47, 1999
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6VOY
 | | Cryo-EM structure of HTLV-1 instasome | | Descriptor: | DNA (25-MER), DNA (5'-D(P*AP*CP*AP*CP*AP*CP*TP*TP*GP*AP*CP*TP*AP*GP*GP*GP*TP*G)-3'), DNA-binding protein 7d, ... | | Authors: | Bhatt, V, Shi, K, Sundborger, A, Aihara, H. | | Deposit date: | 2020-02-01 | | Release date: | 2020-07-01 | | Method: | ELECTRON MICROSCOPY (3.7 Å) | | Cite: | Structural basis of host protein hijacking in human T-cell leukemia virus integration.
Nat Commun, 11, 2020
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6VK5
 | | Crystal Structure of Methylosinus trichosporium OB3b Soluble Methane Monooxygenase Hydroxylase and Regulatory Component Complex | | Descriptor: | 1,2-ETHANEDIOL, BENZOIC ACID, CHLORIDE ION, ... | | Authors: | Jones, J.C, Banerjee, R, Shi, K, Aihara, H, Lipscomb, J.D. | | Deposit date: | 2020-01-18 | | Release date: | 2020-08-05 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (1.86 Å) | | Cite: | Structural Studies of theMethylosinus trichosporiumOB3b Soluble Methane Monooxygenase Hydroxylase and Regulatory Component Complex Reveal a Transient Substrate Tunnel.
Biochemistry, 59, 2020
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6VK7
 | | Crystal Structure of reduced Methylosinus trichosporium OB3b Soluble Methane Monooxygenase Hydroxylase | | Descriptor: | FE (III) ION, Methane monooxygenase, Methane monooxygenase component A alpha chain | | Authors: | Jones, J.C, Banerjee, R, Shi, K, Aihara, H, Lipscomb, J.D. | | Deposit date: | 2020-01-18 | | Release date: | 2020-08-05 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (2.12 Å) | | Cite: | Structural Studies of theMethylosinus trichosporiumOB3b Soluble Methane Monooxygenase Hydroxylase and Regulatory Component Complex Reveal a Transient Substrate Tunnel.
Biochemistry, 59, 2020
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6VK4
 | | Crystal Structure of Methylosinus trichosporium OB3b Soluble Methane Monooxygenase Hydroxylase and Regulatory Component Complex | | Descriptor: | 1,2-ETHANEDIOL, BENZOIC ACID, FE (II) ION, ... | | Authors: | Jones, J.C, Banerjee, R, Shi, K, Aihara, H, Lipscomb, J.D. | | Deposit date: | 2020-01-18 | | Release date: | 2020-08-05 | | Last modified: | 2024-05-22 | | Method: | X-RAY DIFFRACTION (2.35 Å) | | Cite: | Structural Studies of theMethylosinus trichosporiumOB3b Soluble Methane Monooxygenase Hydroxylase and Regulatory Component Complex Reveal a Transient Substrate Tunnel.
Biochemistry, 59, 2020
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6VK8
 | | Crystal Structure of Methylosinus trichosporium OB3b Soluble Methane Monooxygenase Hydroxylase and Regulatory Component Complex with small organic carboxylate at active center | | Descriptor: | 1,2-ETHANEDIOL, BENZOIC ACID, FE (III) ION, ... | | Authors: | Jones, J.C, Banerjee, R, Shi, K, Aihara, H, Lipscomb, J.D. | | Deposit date: | 2020-01-18 | | Release date: | 2020-08-05 | | Last modified: | 2024-03-06 | | Method: | X-RAY DIFFRACTION (2.03 Å) | | Cite: | Structural Studies of theMethylosinus trichosporiumOB3b Soluble Methane Monooxygenase Hydroxylase and Regulatory Component Complex Reveal a Transient Substrate Tunnel.
Biochemistry, 59, 2020
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6VK6
 | | Crystal Structure of Methylosinus trichosporium OB3b Soluble Methane Monooxygenase Hydroxylase | | Descriptor: | 1,2-ETHANEDIOL, CHLORIDE ION, FE (III) ION, ... | | Authors: | Jones, J.C, Banerjee, R, Shi, K, Aihara, H, Lipscomb, J.D. | | Deposit date: | 2020-01-18 | | Release date: | 2020-08-05 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (1.52 Å) | | Cite: | Structural Studies of theMethylosinus trichosporiumOB3b Soluble Methane Monooxygenase Hydroxylase and Regulatory Component Complex Reveal a Transient Substrate Tunnel.
Biochemistry, 59, 2020
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6VW1
 | | Structure of SARS-CoV-2 chimeric receptor-binding domain complexed with its receptor human ACE2 | | Descriptor: | 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... | | Authors: | Shang, J, Ye, G, Shi, K, Wan, Y.S, Aihara, H, Li, F. | | Deposit date: | 2020-02-18 | | Release date: | 2020-03-04 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (2.68 Å) | | Cite: | Structural basis of receptor recognition by SARS-CoV-2.
Nature, 581, 2020
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6CWJ
 | | Crystal structures of cyanuric acid hydrolase from Moorella thermoacetica complexed with 1,3-Acetone Dicarboxylic Acid | | Descriptor: | 1,3-PROPANDIOL, 3-oxopentanedioic acid, ACETATE ION, ... | | Authors: | Shi, K, Aihara, H. | | Deposit date: | 2018-03-30 | | Release date: | 2019-06-12 | | Last modified: | 2023-10-04 | | Method: | X-RAY DIFFRACTION (2.253 Å) | | Cite: | Crystal structures of Moorella thermoacetica cyanuric acid hydrolase reveal conformational flexibility and asymmetry important for catalysis.
Plos One, 14, 2019
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7TV2
 | | X-ray crystal structure of HIV-2 CA protein CTD | | Descriptor: | Capsid protein p24 | | Authors: | Shi, K, Aihara, H. | | Deposit date: | 2022-02-03 | | Release date: | 2023-05-17 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.98 Å) | | Cite: | HIV-2 Immature Particle Morphology Provides Insights into Gag Lattice Stability and Virus Maturation.
J.Mol.Biol., 435, 2023
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6DHJ
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6DT1
 | | Crystal structure of the ligase from bacteriophage T4 complexed with DNA intermediate | | Descriptor: | 2,3-DIHYDROXY-1,4-DITHIOBUTANE, ADENOSINE MONOPHOSPHATE, CHLORIDE ION, ... | | Authors: | Shi, K, Aihara, H. | | Deposit date: | 2018-06-14 | | Release date: | 2018-09-19 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (2.75 Å) | | Cite: | T4 DNA ligase structure reveals a prototypical ATP-dependent ligase with a unique mode of sliding clamp interaction.
Nucleic Acids Res., 46, 2018
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8E14
 | | Cryo-EM structure of Rous sarcoma virus strand transfer complex | | Descriptor: | DNA (42-MER), DNA (5'-D(*AP*AP*TP*GP*TP*TP*GP*TP*CP*TP*TP*AP*TP*GP*CP*AP*AP*TP*AP*CP*TP*C)-3'), DNA (5'-D(*AP*GP*TP*GP*TP*CP*TP*TP*CP*TP*TP*CP*TP*TP*TP*C)-3'), ... | | Authors: | Pandey, K.K, Bera, S, Shi, K, Aihara, H, Grandgenett, D.P. | | Deposit date: | 2022-08-09 | | Release date: | 2023-04-26 | | Last modified: | 2023-10-18 | | Method: | ELECTRON MICROSCOPY (3.36 Å) | | Cite: | Molecular determinants for Rous sarcoma virus intasome assemblies involved in retroviral integration.
J.Biol.Chem., 299, 2023
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8E5D
 | | Crystal structure of double-stranded DNA deaminase toxin DddA in complex with DNA with the target cytosine parked in the major groove | | Descriptor: | DNA (5'-D(*GP*TP*AP*CP*CP*GP*GP*AP*CP*GP*TP*TP*GP*C)-3'), Double-stranded DNA deaminase toxin A, MAGNESIUM ION, ... | | Authors: | Yin, L.L, Shi, K, Aihara, H. | | Deposit date: | 2022-08-21 | | Release date: | 2023-05-24 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.39 Å) | | Cite: | Structural basis of sequence-specific cytosine deamination by double-stranded DNA deaminase toxin DddA.
Nat.Struct.Mol.Biol., 30, 2023
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8E5E
 | | Crystal structure of double-stranded DNA deaminase toxin DddA in complex with DNA with the target cytosine flipped into the active site | | Descriptor: | DNA (5'-D(*GP*CP*AP*AP*CP*GP*TP*CP*CP*GP*GP*TP*AP*C)-3'), DNA (5'-D(*GP*TP*AP*CP*CP*GP*GP*AP*CP*GP*TP*TP*GP*C)-3'), Double-stranded DNA deaminase toxin A, ... | | Authors: | Yin, L.L, Shi, K, Aihara, H. | | Deposit date: | 2022-08-21 | | Release date: | 2023-05-24 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.62 Å) | | Cite: | Structural basis of sequence-specific cytosine deamination by double-stranded DNA deaminase toxin DddA.
Nat.Struct.Mol.Biol., 30, 2023
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6DRT
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8EUO
 | | Hydroxynitrile Lyase from Hevea brasiliensis with Seven Mutations | | Descriptor: | (S)-hydroxynitrile lyase | | Authors: | Greenberg, L.R, Walsh, M.E, Kazlauskas, R.J, Pierce, C.T, Shi, K, Aihara, H, Evans, R.L. | | Deposit date: | 2022-10-19 | | Release date: | 2022-11-30 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.99 Å) | | Cite: | to be published
To Be Published
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8EJO
 | | Crystal structure of the homeodomain of Platypus sDUX in complex with DNA | | Descriptor: | 1,2-ETHANEDIOL, DNA (5'-D(*GP*CP*GP*TP*AP*AP*TP*CP*TP*AP*AP*TP*CP*AP*AP*CP*A)-3'), DNA (5'-D(*TP*GP*TP*TP*GP*AP*TP*TP*AP*GP*AP*TP*TP*AP*CP*GP*C)-3'), ... | | Authors: | Yin, L.L, Shi, K, Aihara, H. | | Deposit date: | 2022-09-18 | | Release date: | 2023-09-20 | | Last modified: | 2023-10-04 | | Method: | X-RAY DIFFRACTION (2.67 Å) | | Cite: | Antagonism among DUX family members evolved from an ancestral toxic single homeodomain protein.
Iscience, 26, 2023
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