7YH7
 
 | | SARS-CoV-2 spike in complex with neutralizing antibody NIV-8 (state 2) | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, NIV-8 Fab heavy chain, ... | | Authors: | Moriyama, S, Anraku, Y, Muranishi, S, Adachi, Y, Kuroda, D, Higuchi, Y, Kotaki, R, Tonouchi, K, Yumoto, K, Suzuki, T, Kita, S, Fukuhara, H, Kuroda, Y, Yamamoto, T, Onodera, T, Fukushi, S, Maeda, K, Nakamura-Uchiyama, F, Hashiguchi, T, Hoshino, A, Maenaka, K, Takahashi, Y. | | Deposit date: | 2022-07-13 | | Release date: | 2023-07-19 | | Last modified: | 2023-10-25 | | Method: | ELECTRON MICROSCOPY (3.3 Å) | | Cite: | Structural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants.
Nat Commun, 14, 2023
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7D7U
 | | Crystal structure of Ago2 MID domain in complex with 8-Br-adenosin-5'-monophosphate | | Descriptor: | 8-BROMO-ADENOSINE-5'-MONOPHOSPHATE, Protein argonaute-2 | | Authors: | Suzuki, M, Takahashi, Y, Saito, J, Miyagi, H, Shinohara, F. | | Deposit date: | 2020-10-06 | | Release date: | 2020-11-25 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | siRNA potency enhancement via chemical modifications of nucleotide bases at the 5'-end of the siRNA guide strand.
Rna, 27, 2021
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3VGW
 | | Crystal structure of monoAc-biotin-avidin complex | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 5-[(3aS,4S,6aR)-1-acetyl-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid, Avidin, ... | | Authors: | Terai, T, Maki, E, Sugiyama, S, Takahashi, Y, Matsumura, H, Mori, Y, Nagano, T. | | Deposit date: | 2011-08-21 | | Release date: | 2011-12-28 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Rational development of caged-biotin protein-labeling agents and some applications in live cells
Chem.Biol., 18, 2011
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3VHH
 | | Crystal structure of DiMe-biotin-avidin complex | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 5-[(3aS,4S,6aR)-1,3-dimethyl-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid, Avidin, ... | | Authors: | Terai, T, Maki, E, Sugiyama, S, Takahashi, Y, Matsumura, H, Mori, Y, Nagano, T. | | Deposit date: | 2011-08-25 | | Release date: | 2011-12-28 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.26 Å) | | Cite: | Rational development of caged-biotin protein-labeling agents and some applications in live cells
Chem.Biol., 18, 2011
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3VHI
 | | Crystal structure of monoZ-biotin-avidin complex | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 5-{(3aS,4S,6aR)-1-[(benzyloxy)carbonyl]-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl}pentanoic acid, Avidin, ... | | Authors: | Terai, T, Maki, E, Sugiyama, S, Takahashi, Y, Matsumura, H, Mori, Y, Nagano, T. | | Deposit date: | 2011-08-25 | | Release date: | 2011-12-28 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.76 Å) | | Cite: | Rational development of caged-biotin protein-labeling agents and some applications in live cells
Chem.Biol., 18, 2011
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3VHM
 | | Crystal structure of NPC-biotin-avidin complex | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 5-[(3aS,4R,6aR)-1-{[(1R)-1-(6-nitro-1,3-benzodioxol-5-yl)ethoxy]carbonyl}-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid, Avidin, ... | | Authors: | Terai, T, Maki, E, Sugiyama, S, Takahashi, Y, Matsumura, H, Mori, Y, Nagano, T. | | Deposit date: | 2011-08-29 | | Release date: | 2011-12-28 | | Last modified: | 2020-07-29 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Rational development of caged-biotin protein-labeling agents and some applications in live cells
Chem.Biol., 18, 2011
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6JZW
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6JZV
 | | Crystal structure of SufU from Bacillus subtilis | | Descriptor: | ZINC ION, Zinc-dependent sulfurtransferase SufU | | Authors: | Fujishiro, T, Takahashi, Y. | | Deposit date: | 2019-05-04 | | Release date: | 2020-05-06 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Zinc-persulfide complex for sulfur mobilization by SufU in SUF-like machinery for Fe-S cluster biosynthesis
to be published
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7WMT
 | | Crystal structure of small molecule 13 bound to human Nicotinamide N-methyltransferase | | Descriptor: | Nicotinamide N-methyltransferase, [(2~{R},4~{S})-4-[2-(aminomethyl)imidazol-1-yl]-2-[1-[(4-chlorophenyl)methyl]-5-methyl-indol-2-yl]pyrrolidin-1-yl]-(1~{H}-pyrrolo[2,3-b]pyridin-5-yl)methanone | | Authors: | Yoshida, S, Uehara, S, Kondo, N, Takahashi, Y, Yamamoto, S, Kameda, A, Kawagoe, S, Inoue, N, Yamada, M, Yoshimura, N, Tachibana, Y. | | Deposit date: | 2022-01-17 | | Release date: | 2022-08-31 | | Method: | X-RAY DIFFRACTION (1.77 Å) | | Cite: | Peptide-to-Small Molecule: A Pharmacophore-Guided Small Molecule Lead Generation Strategy from High-Affinity Macrocyclic Peptides.
J.Med.Chem., 65, 2022
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7WMC
 | | Crystal structure of macrocyclic peptide 1 bound to human Nicotinamide N-methyltransferase | | Descriptor: | Nicotinamide N-methyltransferase, Peptide1 | | Authors: | Yoshida, S, Uehara, S, Kondo, N, Takahashi, Y, Yamamoto, S, Kameda, A, Kawagoe, S, Inoue, N, Yamada, M, Yoshimura, N, Tachibana, Y. | | Deposit date: | 2022-01-14 | | Release date: | 2022-08-31 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (2.55 Å) | | Cite: | Peptide-to-Small Molecule: A Pharmacophore-Guided Small Molecule Lead Generation Strategy from High-Affinity Macrocyclic Peptides.
J.Med.Chem., 65, 2022
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5X9A
 | | Crystal structure of calaxin with calcium | | Descriptor: | 1,2-ETHANEDIOL, CALCIUM ION, Calaxin | | Authors: | Shojima, T, Hou, F, Takahashi, Y, Okai, M, Mizuno, K, Inaba, K, Miyakawa, T, Tanokura, M. | | Deposit date: | 2017-03-06 | | Release date: | 2018-03-14 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (1.85 Å) | | Cite: | Crystal structure of a Ca2+-dependent regulator of flagellar motility reveals the open-closed structural transition
Sci Rep, 8, 2018
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5YPX
 | | Crystal structure of calaxin with magnesium | | Descriptor: | Calaxin, MAGNESIUM ION | | Authors: | Shojima, T, Hou, F, Takahashi, Y, Okai, M, Mizuno, K, Inaba, K, Miyakawa, T, Tanokura, M. | | Deposit date: | 2017-11-04 | | Release date: | 2018-03-14 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (2.64 Å) | | Cite: | Crystal structure of a Ca2+-dependent regulator of flagellar motility reveals the open-closed structural transition
Sci Rep, 8, 2018
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3VOT
 | | Crystal structure of L-amino acid ligase from Bacillus licheniformis | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, CALCIUM ION, CHLORIDE ION, ... | | Authors: | Suzuki, M, Takahashi, Y, Noguchi, A, Arai, T, Yagasaki, M, Kino, K, Saito, J. | | Deposit date: | 2012-02-08 | | Release date: | 2012-11-07 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | The structure of L-amino-acid ligase from Bacillus licheniformis
Acta Crystallogr.,Sect.D, 68, 2012
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7C6A
 | | Crystal structure of AT2R-BRIL and SRP2070_Fab complex | | Descriptor: | IgG Light Chain, IgG heavy chain, SAR1, ... | | Authors: | Suzuki, M, Miyagi, H, Asada, H, Yasunaga, M, Suno, C, Takahashi, Y, Saito, J, Iwata, S. | | Deposit date: | 2020-05-21 | | Release date: | 2020-07-29 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (3.4 Å) | | Cite: | The discovery of a new antibody for BRIL-fused GPCR structure determination.
Sci Rep, 10, 2020
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7C61
 | | Crystal structure of 5-HT1B-BRIL and SRP2070_Fab complex | | Descriptor: | 5-hydroxytryptamine receptor 1B,Soluble cytochrome b562,5-hydroxytryptamine receptor 1B, Ergotamine, IGG HEAVY CHAIN, ... | | Authors: | Suzuki, M, Miyagi, H, Asada, H, Yasunaga, M, Suno, C, Takahashi, Y, Saito, J, Iwata, S. | | Deposit date: | 2020-05-21 | | Release date: | 2020-07-29 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | The discovery of a new antibody for BRIL-fused GPCR structure determination.
Sci Rep, 10, 2020
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7C8M
 | | Crystal structure of IscU wild-type | | Descriptor: | FE2/S2 (INORGANIC) CLUSTER, Nitrogen-fixing NifU domain protein | | Authors: | Kunichika, K, Takahashi, Y, Fujishiro, T. | | Deposit date: | 2020-06-03 | | Release date: | 2021-05-26 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (3.5 Å) | | Cite: | The Structure of the Dimeric State of IscU Harboring Two Adjacent [2Fe-2S] Clusters Provides Mechanistic Insights into Cluster Conversion to [4Fe-4S].
Biochemistry, 60, 2021
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7C8N
 | | Crystal structure of IscU H106A variant | | Descriptor: | FE2/S2 (INORGANIC) CLUSTER, Nitrogen-fixing NifU domain protein | | Authors: | Kunichika, K, Takahashi, Y, Fujishiro, T. | | Deposit date: | 2020-06-03 | | Release date: | 2021-05-26 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | The Structure of the Dimeric State of IscU Harboring Two Adjacent [2Fe-2S] Clusters Provides Mechanistic Insights into Cluster Conversion to [4Fe-4S].
Biochemistry, 60, 2021
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7C8O
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7CET
 | | Crystal structure of D-cycloserine-bound form of cysteine desulfurase NifS from Helicobacter pylori | | Descriptor: | (5-hydroxy-6-methyl-4-{[(3-oxo-2,3-dihydro-1,2-oxazol-4-yl)amino]methyl}pyridin-3-yl)methyl dihydrogen phosphate, CHLORIDE ION, Cysteine desulfurase IscS, ... | | Authors: | Nakamura, R, Takahashi, Y, Fujishiro, T. | | Deposit date: | 2020-06-24 | | Release date: | 2021-06-30 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.64 Å) | | Cite: | Cycloserine enantiomers inhibit PLP-dependent cysteine desulfurase SufS via distinct mechanisms.
Febs J., 2022
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7CEQ
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7CER
 | | Crystal structure of D-cycloserine-bound form of cysteine desulfurase SufS H121A from Bacillus subtilis | | Descriptor: | Cysteine desulfurase SufS, D-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-N,O-CYCLOSERYLAMIDE, DI(HYDROXYETHYL)ETHER, ... | | Authors: | Nakamura, R, Takahashi, Y, Fujishiro, T. | | Deposit date: | 2020-06-24 | | Release date: | 2021-06-30 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Cycloserine enantiomers inhibit PLP-dependent cysteine desulfurase SufS via distinct mechanisms.
Febs J., 2022
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7CEU
 | | Crystal structure of L-cycloserine-bound form of cysteine desulfurase NifS from Helicobacter pylori | | Descriptor: | (5-hydroxy-6-methyl-4-{[(3-oxo-2,3-dihydro-1,2-oxazol-4-yl)amino]methyl}pyridin-3-yl)methyl dihydrogen phosphate, Cysteine desulfurase IscS, ISOPROPYL ALCOHOL | | Authors: | Nakamura, R, Takahashi, Y, Fujishiro, T. | | Deposit date: | 2020-06-24 | | Release date: | 2021-06-30 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.9 Å) | | Cite: | Cycloserine enantiomers inhibit PLP-dependent cysteine desulfurase SufS via distinct mechanisms.
Febs J., 2022
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7CES
 | | Crystal structure of L-cycloserine-bound form of cysteine desulfurase SufS H121A from Bacillus subtilis | | Descriptor: | (5-hydroxy-6-methyl-4-{[(3-oxo-2,3-dihydro-1,2-oxazol-4-yl)amino]methyl}pyridin-3-yl)methyl dihydrogen phosphate, Cysteine desulfurase SufS, DI(HYDROXYETHYL)ETHER | | Authors: | Nakamura, R, Takahashi, Y, Fujishiro, T. | | Deposit date: | 2020-06-24 | | Release date: | 2021-06-30 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Cycloserine enantiomers inhibit PLP-dependent cysteine desulfurase SufS via distinct mechanisms.
Febs J., 2022
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7CEO
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7CNV
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