8IC8
 
 | | Exo-alpha-D-arabinofuranosidase from Microbacterium arabinogalactanolyticum | | Descriptor: | Exo-alpha-D-arabinofuranosidase, PHOSPHATE ION | | Authors: | Kashima, T, Arakawa, T, Yamada, C, Ishiwata, A, Fujita, K, Fushinobu, S. | | Deposit date: | 2023-02-11 | | Release date: | 2023-08-16 | | Last modified: | 2023-09-27 | | Method: | X-RAY DIFFRACTION (2.42 Å) | | Cite: | Identification and characterization of endo-alpha-, exo-alpha-, and exo-beta-D-arabinofuranosidases degrading lipoarabinomannan and arabinogalactan of mycobacteria.
Nat Commun, 14, 2023
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5JNT
 | | Crystal structure of human low molecular weight protein tyrosine phosphatase (LMPTP) type A complexed with MES | | Descriptor: | 1,2-ETHANEDIOL, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, DIMETHYL SULFOXIDE, ... | | Authors: | Stanford, S.M, Aleshin, A.E, Liddington, R.C, Bankston, L, Cadwell, G, Bottini, N. | | Deposit date: | 2016-04-30 | | Release date: | 2017-03-29 | | Last modified: | 2023-09-27 | | Method: | X-RAY DIFFRACTION (1.45 Å) | | Cite: | Diabetes reversal by inhibition of the low-molecular-weight tyrosine phosphatase.
Nat. Chem. Biol., 13, 2017
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5JNR
 | | Crystal structure of human low molecular weight protein tyrosine phosphatase (LMPTP) type A | | Descriptor: | Low molecular weight phosphotyrosine protein phosphatase | | Authors: | Stanford, S.M, Aleshin, A.E, Liddington, R.C, Bankston, L, Cadwell, G, Bottini, N. | | Deposit date: | 2016-04-30 | | Release date: | 2017-03-29 | | Last modified: | 2023-09-27 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Diabetes reversal by inhibition of the low-molecular-weight tyrosine phosphatase.
Nat. Chem. Biol., 13, 2017
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5Y5M
 | | SFX structure of cytochrome P450nor: a complete dark data without pump laser (resting state) | | Descriptor: | NADP nitrous oxide-forming nitric oxide reductase, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Tosha, T, Nomura, T, Nishida, T, Saeki, N, Okubayashi, K, Yamagiwa, R, Sugahara, M, Nakane, T, Yamashita, K, Hirata, K, Ueno, G, Kimura, T, Hisano, T, Muramoto, K, Sawai, H, Takeda, H, Mizohata, E, Yamashita, A, Kanematsu, Y, Takano, Y, Nango, E, Tanaka, R, Nureki, O, Ikemoto, Y, Murakami, H, Owada, S, Tono, K, Yabashi, M, Yamamoto, M, Ago, H, Iwata, S, Sugimoto, H, Shiro, Y, Kubo, M. | | Deposit date: | 2017-08-09 | | Release date: | 2018-08-08 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.
Nat Commun, 8, 2017
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5Y5L
 | | Time-resolved SFX structure of cytochrome P450nor: dark-2 data in the absence of NADH (resting state) | | Descriptor: | NADP nitrous oxide-forming nitric oxide reductase, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Tosha, T, Nomura, T, Nishida, T, Saeki, N, Okubayashi, K, Yamagiwa, R, Sugahara, M, Nakane, T, Yamashita, K, Hirata, K, Ueno, G, Kimura, T, Hisano, T, Muramoto, K, Sawai, H, Takeda, H, Mizohata, E, Yamashita, A, Kanematsu, Y, Takano, Y, Nango, E, Tanaka, R, Nureki, O, Ikemoto, Y, Murakami, H, Owada, S, Tono, K, Yabashi, M, Yamamoto, M, Ago, H, Iwata, S, Sugimoto, H, Shiro, Y, Kubo, M. | | Deposit date: | 2017-08-09 | | Release date: | 2017-12-06 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.
Nat Commun, 8, 2017
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5Y5I
 | | Time-resolved SFX structure of cytochrome P450nor: 20 ms after photo-irradiation of caged NO in the presence of NADH (NO-bound state), light data | | Descriptor: | GLYCEROL, NADP nitrous oxide-forming nitric oxide reductase, NITRIC OXIDE, ... | | Authors: | Tosha, T, Nomura, T, Nishida, T, Saeki, N, Okubayashi, K, Yamagiwa, R, Sugahara, M, Nakane, T, Yamashita, K, Hirata, K, Ueno, G, Kimura, T, Hisano, T, Muramoto, K, Sawai, H, Takeda, H, Mizohata, E, Yamashita, A, Kanematsu, Y, Takano, Y, Nango, E, Tanaka, R, Nureki, O, Ikemoto, Y, Murakami, H, Owada, S, Tono, K, Yabashi, M, Yamamoto, M, Ago, H, Iwata, S, Sugimoto, H, Shiro, Y, Kubo, M. | | Deposit date: | 2017-08-09 | | Release date: | 2017-12-06 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.
Nat Commun, 8, 2017
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5Y5J
 | | Time-resolved SFX structure of cytochrome P450nor: dark-2 data in the presence of NADH (resting state) | | Descriptor: | GLYCEROL, NADP nitrous oxide-forming nitric oxide reductase, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Tosha, T, Nomura, T, Nishida, T, Saeki, N, Okubayashi, K, Yamagiwa, R, Sugahara, M, Nakane, T, Yamashita, K, Hirata, K, Ueno, G, Kimura, T, Hisano, T, Muramoto, K, Sawai, H, Takeda, H, Mizohata, E, Yamashita, A, Kanematsu, Y, Takano, Y, Nango, E, Tanaka, R, Nureki, O, Ikemoto, Y, Murakami, H, Owada, S, Tono, K, Yabashi, M, Yamamoto, M, Ago, H, Iwata, S, Sugimoto, H, Shiro, Y, Kubo, M. | | Deposit date: | 2017-08-09 | | Release date: | 2017-12-06 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.
Nat Commun, 8, 2017
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5Y5K
 | | Time-resolved SFX structure of cytochrome P450nor : 20 ms after photo-irradiation of caged NO in the absence of NADH (NO-bound state), light data | | Descriptor: | NADP nitrous oxide-forming nitric oxide reductase, NITRIC OXIDE, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Tosha, T, Nomura, T, Nishida, T, Saeki, N, Okubayashi, K, Yamagiwa, R, Sugahara, M, Nakane, T, Yamashita, K, Hirata, K, Ueno, G, Kimura, T, Hisano, T, Muramoto, K, Sawai, H, Takeda, H, Mizohata, E, Yamashita, A, Kanematsu, Y, Takano, Y, Nango, E, Tanaka, R, Nureki, O, Ikemoto, Y, Murakami, H, Owada, S, Tono, K, Yabashi, M, Yamamoto, M, Ago, H, Iwata, S, Sugimoto, H, Shiro, Y, Kubo, M. | | Deposit date: | 2017-08-09 | | Release date: | 2017-12-06 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.
Nat Commun, 8, 2017
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5Y5H
 | | SF-ROX structure of cytochrome P450nor (NO-bound state) determined at SACLA | | Descriptor: | GLYCEROL, NADP nitrous oxide-forming nitric oxide reductase, NITRIC OXIDE, ... | | Authors: | Tosha, T, Nomura, T, Nishida, T, Yamagiwa, R, Yamashita, K, Hirata, K, Ueno, G, Kimura, T, Hisano, T, Muramoto, K, Sawai, H, Takeda, H, Yamashita, A, Murakami, H, Owada, S, Tono, K, Yabashi, M, Yamamoto, M, Ago, H, Sugimoto, H, Shiro, Y, Kubo, M. | | Deposit date: | 2017-08-09 | | Release date: | 2017-12-06 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.
Nat Commun, 8, 2017
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7ZMJ
 | | SFX structure of dye-type peroxidase DtpB R243A variant in the ferric state | | Descriptor: | MAGNESIUM ION, PROTOPORPHYRIN IX CONTAINING FE, Putative dye-decolorizing peroxidase (DyP), ... | | Authors: | Lucic, M, Worrall, J.A.R, Hough, M.A, Shilova, A, Axford, D.A, Owen, R.L, Tosha, T, Sugimoto, H, Owada, S. | | Deposit date: | 2022-04-19 | | Release date: | 2022-12-07 | | Last modified: | 2024-01-31 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Serial Femtosecond Crystallography Reveals the Role of Water in the One- or Two-Electron Redox Chemistry of Compound I in the Catalytic Cycle of the B-Type Dye-Decolorizing Peroxidase DtpB.
Acs Catalysis, 12, 2022
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2HOQ
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7F8J
 | | Cryo-EM structure of human pannexin-1 in a nanodisc | | Descriptor: | 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, Pannexin-1 | | Authors: | Kuzuya, M, Hirano, H, Hayashida, K, Watanabe, M, Kobayashi, K, Tani, K, Fujiyoshi, Y, Oshima, A. | | Deposit date: | 2021-07-02 | | Release date: | 2022-01-26 | | Last modified: | 2022-02-23 | | Method: | ELECTRON MICROSCOPY (3.6 Å) | | Cite: | Structures of human pannexin-1 in nanodiscs reveal gating mediated by dynamic movement of the N terminus and phospholipids.
Sci.Signal., 15, 2022
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7F8O
 | | Cryo-EM structure of the C-terminal deletion mutant of human PANX1 in a nanodisc | | Descriptor: | 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, Pannexin-1 | | Authors: | Kuzuya, M, Hirano, H, Hayashida, K, Watanabe, M, Kobayashi, K, Tani, K, Fujiyoshi, Y, Oshima, A. | | Deposit date: | 2021-07-02 | | Release date: | 2022-01-26 | | Last modified: | 2022-02-23 | | Method: | ELECTRON MICROSCOPY (3.6 Å) | | Cite: | Structures of human pannexin-1 in nanodiscs reveal gating mediated by dynamic movement of the N terminus and phospholipids.
Sci.Signal., 15, 2022
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3W7U
 | | Escherichia coli K12 YgjK complexed with galactose | | Descriptor: | CALCIUM ION, Uncharacterized protein YgjK, alpha-D-galactopyranose | | Authors: | Miyazaki, T, Kurakata, Y, Uechi, A, Yoshida, H, Kamitori, S, Sakano, Y, Nishikawa, A, Tonozuka, T. | | Deposit date: | 2013-03-06 | | Release date: | 2013-04-03 | | Last modified: | 2020-07-29 | | Method: | X-RAY DIFFRACTION (1.99 Å) | | Cite: | Structural insights into the substrate specificity and function of Escherichia coli K12 YgjK, a glucosidase belonging to the glycoside hydrolase family 63.
J.Mol.Biol., 381, 2008
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3WWG
 | | Crystal structure of the N-glycan-deficient variant N448A of isopullulanase complexed with isopanose | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, Isopullulanase, alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose, ... | | Authors: | Miyazaki, T, Yashiro, H, Nishikawa, A, Tonozuka, T. | | Deposit date: | 2014-06-17 | | Release date: | 2014-11-12 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | The side chain of a glycosylated asparagine residue is important for the stability of isopullulanase
J.Biochem., 157, 2015
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7F8N
 | | Human pannexin-1 showing a conformational change in the N-terminal domain and blocked pore | | Descriptor: | 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, Pannexin-1 | | Authors: | Kuzuya, M, Hirano, H, Hayashida, K, Watanabe, M, Kobayashi, K, Tani, K, Fujiyoshi, Y, Oshima, A. | | Deposit date: | 2021-07-02 | | Release date: | 2022-01-26 | | Last modified: | 2022-02-23 | | Method: | ELECTRON MICROSCOPY (3.4 Å) | | Cite: | Structures of human pannexin-1 in nanodiscs reveal gating mediated by dynamic movement of the N terminus and phospholipids.
Sci.Signal., 15, 2022
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6PS3
 | | XFEL beta2 AR structure by ligand exchange from Timolol to Carvedilol. | | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, (2S)-1-(8H-CARBAZOL-4-YLOXY)-3-[2-(2-METHOXYPHENOXY)ETHYLAMINO]PROPAN-2-OL, CHOLESTEROL, ... | | Authors: | Ishchenko, A, Stauch, B, Han, G.W, Batyuk, A, Shiriaeva, A, Li, C, Zatsepin, N.A, Weierstall, U, Liu, W, Nango, E, Nakane, T, Tanaka, R, Tono, K, Joti, Y, Iwata, S, Moraes, I, Gati, C, Cherezov, C. | | Deposit date: | 2019-07-12 | | Release date: | 2019-11-13 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Toward G protein-coupled receptor structure-based drug design using X-ray lasers.
Iucrj, 6, 2019
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6PS6
 | | XFEL beta2 AR structure by ligand exchange from Timolol to Timolol. | | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, (2S)-1-(tert-butylamino)-3-[(4-morpholin-4-yl-1,2,5-thiadiazol-3-yl)oxy]propan-2-ol, CHOLESTEROL, ... | | Authors: | Ishchenko, A, Stauch, B, Han, G.W, Batyuk, A, Shiriaeva, A, Li, C, Zatsepin, N.A, Weierstall, U, Liu, W, Nango, E, Nakane, T, Tanaka, R, Tono, K, Joti, Y, Iwata, S, Moraes, I, Gati, C, Cherezov, C. | | Deposit date: | 2019-07-12 | | Release date: | 2019-11-13 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Toward G protein-coupled receptor structure-based drug design using X-ray lasers.
Iucrj, 6, 2019
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6PS4
 | | XFEL beta2 AR structure by ligand exchange from Timolol to ICI-118551. | | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, (2S,3S)-1-[(7-methyl-2,3-dihydro-1H-inden-4-yl)oxy]-3-[(1-methylethyl)amino]butan-2-ol, CHOLESTEROL, ... | | Authors: | Ishchenko, A, Stauch, B, Han, G.W, Batyuk, A, Shiriaeva, A, Li, C, Zatsepin, N.A, Weierstall, U, Liu, W, Nango, E, Nakane, T, Tanaka, R, Tono, K, Joti, Y, Iwata, S, Moraes, I, Gati, C, Cherezov, C. | | Deposit date: | 2019-07-12 | | Release date: | 2019-11-13 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Toward G protein-coupled receptor structure-based drug design using X-ray lasers.
Iucrj, 6, 2019
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6PS1
 | | XFEL beta2 AR structure by ligand exchange from Alprenolol to Timolol. | | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, (2S)-1-(tert-butylamino)-3-[(4-morpholin-4-yl-1,2,5-thiadiazol-3-yl)oxy]propan-2-ol, CHOLESTEROL, ... | | Authors: | Ishchenko, A, Stauch, B, Han, G.W, Batyuk, A, Shiriaeva, A, Li, C, Zatsepin, N.A, Weierstall, U, Liu, W, Nango, E, Nakane, T, Tanaka, R, Tono, K, Joti, Y, Iwata, S, Moraes, I, Gati, C, Cherezov, C. | | Deposit date: | 2019-07-12 | | Release date: | 2019-11-13 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (3.2 Å) | | Cite: | Toward G protein-coupled receptor structure-based drug design using X-ray lasers.
Iucrj, 6, 2019
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8IJW
 | | Cryo-EM structure of the gastric proton pump with bound DQ-06 | | Descriptor: | 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE, 2-acetamido-2-deoxy-beta-D-glucopyranose, CHOLESTEROL, ... | | Authors: | Abe, K, Yokoshima, S, Yoshimori, A. | | Deposit date: | 2023-02-28 | | Release date: | 2023-08-30 | | Last modified: | 2023-10-04 | | Method: | ELECTRON MICROSCOPY (2.19 Å) | | Cite: | Deep learning driven de novo drug design based on gastric proton pump structures.
Commun Biol, 6, 2023
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8IJV
 | | Cryo-EM structure of the gastric proton pump with bound DQ-02 | | Descriptor: | 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE, 2-acetamido-2-deoxy-beta-D-glucopyranose, 4-[[5-chloranyl-2-(4-chlorophenyl)phenyl]methoxy]-N-methyl-but-2-yn-1-amine, ... | | Authors: | Abe, K, Yokoshima, S, Yoshimori, A. | | Deposit date: | 2023-02-28 | | Release date: | 2023-08-30 | | Last modified: | 2023-10-04 | | Method: | ELECTRON MICROSCOPY (2.1 Å) | | Cite: | Deep learning driven de novo drug design based on gastric proton pump structures.
Commun Biol, 6, 2023
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8IJX
 | | Cryo-EM structure of the gastric proton pump with bound DQ-18 | | Descriptor: | 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE, 1-[4-[(5-chloranyl-2-phenylmethoxy-phenyl)methoxy]phenyl]-N-methyl-methanamine, 2-acetamido-2-deoxy-beta-D-glucopyranose, ... | | Authors: | Abe, K, Yokoshima, S, Yoshimori, A. | | Deposit date: | 2023-02-28 | | Release date: | 2023-08-30 | | Last modified: | 2023-10-04 | | Method: | ELECTRON MICROSCOPY (2.08 Å) | | Cite: | Deep learning driven de novo drug design based on gastric proton pump structures.
Commun Biol, 6, 2023
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3W9A
 | | Crystal structure of the catalytic domain of the glycoside hydrolase family 131 protein from Coprinopsis cinerea | | Descriptor: | GLYCEROL, Putative uncharacterized protein | | Authors: | Miyazaki, T, Tanaka, Y, Tamura, M, Yoshida, M, Nishikawa, A, Tonozuka, T. | | Deposit date: | 2013-04-01 | | Release date: | 2013-05-22 | | Last modified: | 2013-07-10 | | Method: | X-RAY DIFFRACTION (1.99 Å) | | Cite: | Crystal structure of the N-terminal domain of a glycoside hydrolase family 131 protein from Coprinopsis cinerea
Febs Lett., 587, 2013
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4PZN
 | | Crystal structure of PHC3 SAM L971E | | Descriptor: | 1,2-ETHANEDIOL, Polyhomeotic-like protein 3 | | Authors: | Nanyes, D.R, Junco, S.E, Taylor, A.B, Robinson, A.K, Patterson, N.L, Shivarajpur, A, Halloran, J, Hale, S.M, Kaur, Y, Hart, P.J, Kim, C.A. | | Deposit date: | 2014-03-31 | | Release date: | 2014-07-30 | | Last modified: | 2023-09-20 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Multiple polymer architectures of human polyhomeotic homolog 3 sterile alpha motif.
Proteins, 82, 2014
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