7XUC
 
 | | Structure of G9a in complex with compound 11a | | Descriptor: | 1,2-ETHANEDIOL, 3,6,6-trimethyl-4-oxidanylidene-~{N}-[(2~{S})-1-oxidanylidene-1-phenylazanyl-hexan-2-yl]-5,7-dihydro-1~{H}-indole-2-carboxamide, CHLORIDE ION, ... | | Authors: | Niwa, H, Shirai, F, Sato, S, Nishigaya, Y, Umehara, T. | | Deposit date: | 2022-05-18 | | Release date: | 2023-03-29 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.67 Å) | | Cite: | Discovery of Novel Substrate-Competitive Lysine Methyltransferase G9a Inhibitors as Anticancer Agents.
J.Med.Chem., 66, 2023
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7XUB
 | | Structure of G9a in complex with compound 10d | | Descriptor: | 1,2-ETHANEDIOL, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, Histone-lysine N-methyltransferase EHMT2, ... | | Authors: | Niwa, H, Shirai, F, Sato, S, Nishigaya, Y, Umehara, T. | | Deposit date: | 2022-05-18 | | Release date: | 2023-03-29 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Discovery of Novel Substrate-Competitive Lysine Methyltransferase G9a Inhibitors as Anticancer Agents.
J.Med.Chem., 66, 2023
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1SE0
 | | Crystal structure of DIAP1 BIR1 bound to a Grim peptide | | Descriptor: | Apoptosis 1 inhibitor, Cell death protein Grim, ZINC ION | | Authors: | Yan, N, Wu, J.W, Shi, Y. | | Deposit date: | 2004-02-15 | | Release date: | 2004-04-27 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (1.75 Å) | | Cite: | Molecular mechanisms of DrICE inhibition by DIAP1 and removal of inhibition by Reaper, Hid and Grim.
Nat.Struct.Mol.Biol., 11, 2004
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1TY4
 | | Crystal structure of a CED-9/EGL-1 complex | | Descriptor: | Apoptosis regulator ced-9, EGg Laying defective EGL-1, programmed cell death activator | | Authors: | Yan, N, Gu, L, Kokel, D, Xue, D, Shi, Y. | | Deposit date: | 2004-07-07 | | Release date: | 2004-09-28 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Structural, Biochemical, and Functional Analyses of CED-9 Recognition by the Proapoptotic Proteins EGL-1 and CED-4
Mol.Cell, 15, 2004
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1SDZ
 | | Crystal structure of DIAP1 BIR1 bound to a Reaper peptide | | Descriptor: | Apoptosis 1 inhibitor, Reaper, ZINC ION | | Authors: | Yan, N, Wu, J.W, Shi, Y. | | Deposit date: | 2004-02-15 | | Release date: | 2004-04-27 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (1.78 Å) | | Cite: | Molecular mechanisms of DrICE inhibition by DIAP1 and removal of inhibition by Reaper, Hid and Grim.
Nat.Struct.Mol.Biol., 11, 2004
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6JU4
 | | Aspergillus oryzae pro-tyrosinase F513Y mutant | | Descriptor: | COPPER (II) ION, Tyrosinase | | Authors: | Fujieda, N, Umakoshi, K, Nishikawa, Y, Kurisu, G, Itoh, S. | | Deposit date: | 2019-04-13 | | Release date: | 2020-05-13 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.35 Å) | | Cite: | Copper-Oxygen Dynamics in the Tyrosinase Mechanism.
Angew.Chem.Int.Ed.Engl., 59, 2020
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6JUB
 | | Radiation damage in Aspergillus oryzae pro-tyrosinase oxygen-bound C92A mutant | | Descriptor: | COPPER (II) ION, PEROXIDE ION, Tyrosinase | | Authors: | Fujieda, N, Umakoshi, K, Nishikawa, Y, Kurisu, G, Itoh, S. | | Deposit date: | 2019-04-13 | | Release date: | 2020-05-13 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.54 Å) | | Cite: | Copper-Oxygen Dynamics in the Tyrosinase Mechanism.
Angew.Chem.Int.Ed.Engl., 59, 2020
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6JU8
 | | Aspergillus oryzae active-tyrosinase copper-bound C92A mutant | | Descriptor: | COPPER (II) ION, NITRATE ION, Tyrosinase | | Authors: | Fujieda, N, Umakoshi, K, Nishikawa, Y, Kurisu, G, Itoh, S. | | Deposit date: | 2019-04-13 | | Release date: | 2020-05-13 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.27 Å) | | Cite: | Copper-Oxygen Dynamics in the Tyrosinase Mechanism.
Angew.Chem.Int.Ed.Engl., 59, 2020
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6KXE
 | | The ishigamide ketosynthase/chain length factor | | Descriptor: | 1,2-ETHANEDIOL, ACETATE ION, Ketosynthase, ... | | Authors: | Du, D, Katsuyama, Y, Horiuchi, M, Fushinobu, S, Chen, A, Davis, T, Burkart, M, Ohnishi, Y. | | Deposit date: | 2019-09-10 | | Release date: | 2020-05-06 | | Last modified: | 2020-07-08 | | Method: | X-RAY DIFFRACTION (1.81 Å) | | Cite: | Structural basis for selectivity in a highly reducing type II polyketide synthase.
Nat.Chem.Biol., 16, 2020
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6KXF
 | | The ishigamide ketosynthase/chain length factor | | Descriptor: | ACP, Ketosynthase, [(3~{R})-2,2-dimethyl-4-[[3-[2-[[(~{E})-oct-2-enoyl]amino]ethylamino]-3-oxidanylidene-propyl]amino]-3-oxidanyl-4-oxidanylidene-butyl] dihydrogen phosphate | | Authors: | Du, D, Katsuyama, Y, Horiuchi, M, Fushinobu, S, Chen, A, Davis, T, Burkart, M, Ohnishi, Y. | | Deposit date: | 2019-09-10 | | Release date: | 2020-05-06 | | Last modified: | 2020-07-08 | | Method: | X-RAY DIFFRACTION (1.98 Å) | | Cite: | Structural basis for selectivity in a highly reducing type II polyketide synthase.
Nat.Chem.Biol., 16, 2020
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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, Someya, T, 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: | 2024-05-15 | | 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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7YH6
 | | Structure of SARS-CoV-2 spike RBD in complex with neutralizing antibody NIV-8 | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, NIV-8 Fab heavy chain, NIV-8 Fab light chain, ... | | Authors: | Moriyama, S, Anraku, Y, Muranishi, S, Adachi, Y, Kuroda, D, Higuchi, Y, Kotaki, R, Tonouchi, K, Yumoto, K, Suzuki, T, Kita, S, Someya, T, 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: | 2022-07-12 | | Release date: | 2023-07-19 | | Last modified: | 2024-05-15 | | Method: | ELECTRON MICROSCOPY (3.4 Å) | | Cite: | Structural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants.
Nat Commun, 14, 2023
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6KNB
 | | PolD-PCNA-DNA (form A) | | Descriptor: | DNA polymerase D DP2 (DNA polymerase II large) subunit, DNA polymerase II small subunit, DNA polymerase sliding clamp 1, ... | | Authors: | Mayanagi, K, Oki, K, Miyazaki, N, Ishino, S, Yamagami, T, Iwasaki, K, Kohda, D, Morikawa, K, Shirai, T, Ishino, Y. | | Deposit date: | 2019-08-05 | | Release date: | 2020-08-05 | | Last modified: | 2021-02-17 | | Method: | ELECTRON MICROSCOPY (6.9 Å) | | Cite: | Two conformations of DNA polymerase D-PCNA-DNA, an archaeal replisome complex, revealed by cryo-electron microscopy.
Bmc Biol., 18, 2020
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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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6KFZ
 | | SufS from Bacillus subtilis, soaked with L-cysteine for 90 sec at 1.96 angstrom resolution | | Descriptor: | Cysteine desulfurase SufS, DI(HYDROXYETHYL)ETHER, N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-L-CYSTEINE | | Authors: | Nakamura, R, Takahashi, Y, Fujishiro, T. | | Deposit date: | 2019-07-09 | | Release date: | 2019-10-16 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.96 Å) | | Cite: | Snapshots of PLP-substrate and PLP-product external aldimines as intermediates in two types of cysteine desulfurase enzymes.
Febs J., 287, 2020
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5DFZ
 | | Structure of Vps34 complex II from S. cerevisiae. | | Descriptor: | Nanobody binding S. cerevisiae Vps34, Phosphatidylinositol 3-kinase VPS34, Putative N-terminal domain of S. cerevisiae Vps30, ... | | Authors: | Rostislavleva, K, Soler, N, Ohashi, Y, Zhang, L, Williams, R.L. | | Deposit date: | 2015-08-27 | | Release date: | 2015-10-07 | | Last modified: | 2024-05-08 | | Method: | X-RAY DIFFRACTION (4.4 Å) | | Cite: | Structure and flexibility of the endosomal Vps34 complex reveals the basis of its function on membranes.
Science, 350, 2015
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4FRU
 | | Crystal structure of horse wild-type cyclophilin B | | Descriptor: | 1-ETHOXY-2-(2-METHOXYETHOXY)ETHANE, DI(HYDROXYETHYL)ETHER, Peptidyl-prolyl cis-trans isomerase, ... | | Authors: | Boudko, S.P, Ishikawa, Y, Bachinger, H.P. | | Deposit date: | 2012-06-26 | | Release date: | 2012-11-14 | | Last modified: | 2023-09-13 | | Method: | X-RAY DIFFRACTION (1.1 Å) | | Cite: | Crystal structures of wild-type and mutated cyclophilin B that causes hyperelastosis cutis in the American quarter horse.
BMC Res Notes, 5, 2012
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6KFF
 | | Undocked INX-6 hemichannel in a nanodisc | | Descriptor: | Innexin-6 | | Authors: | Burendei, B, Shinozaki, R, Watanabe, M, Terada, T, Tani, K, Fujiyoshi, Y, Oshima, A. | | Deposit date: | 2019-07-07 | | Release date: | 2020-02-12 | | Last modified: | 2020-03-11 | | Method: | ELECTRON MICROSCOPY (3.8 Å) | | Cite: | Cryo-EM structures of undocked innexin-6 hemichannels in phospholipids.
Sci Adv, 6, 2020
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6KFH
 | | Undocked hemichannel of an N-terminal deletion mutant of INX-6 in a nanodisc | | Descriptor: | Innexin-6 | | Authors: | Burendei, B, Shinozaki, R, Watanabe, M, Terada, T, Tani, K, Fujiyoshi, Y, Oshima, A. | | Deposit date: | 2019-07-07 | | Release date: | 2020-02-12 | | Last modified: | 2020-03-11 | | Method: | ELECTRON MICROSCOPY (3.6 Å) | | Cite: | Cryo-EM structures of undocked innexin-6 hemichannels in phospholipids.
Sci Adv, 6, 2020
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6QQ5
 | | Cryo-EM structure of dimeric quinol dependent nitric oxide reductase (qNOR) from Alcaligenes xylosoxidans | | Descriptor: | CALCIUM ION, FE (III) ION, Nitric oxide reductase subunit B, ... | | Authors: | Gopalasingam, C.C, Johnson, R.M, Chiduza, G.N, Tosha, T, Yamamoto, M, Shiro, Y, Antonyuk, S.V, Muench, S.P, Hasnain, S.S. | | Deposit date: | 2019-02-17 | | Release date: | 2019-09-11 | | Last modified: | 2024-05-15 | | Method: | ELECTRON MICROSCOPY (3.9 Å) | | Cite: | Dimeric structures of quinol-dependent nitric oxide reductases (qNORs) revealed by cryo-electron microscopy.
Sci Adv, 5, 2019
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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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