2DEP
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![BU of 2dep by Molmil](/molmil-images/mine/2dep) | |
4WH2
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![BU of 4wh2 by Molmil](/molmil-images/mine/4wh2) | N-acetylhexosamine 1-kinase in complex with ADP | Descriptor: | ACETIC ACID, ADENOSINE-5'-DIPHOSPHATE, GLYCEROL, ... | Authors: | Sato, M, Arakawa, T, Nam, Y.W, Nishimoto, M, Kitaoka, M, Fushinobu, S. | Deposit date: | 2014-09-19 | Release date: | 2015-02-18 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (1.847 Å) | Cite: | Open-close structural change upon ligand binding and two magnesium ions required for the catalysis of N-acetylhexosamine 1-kinase Biochim.Biophys.Acta, 1854, 2015
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4WH1
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![BU of 4wh1 by Molmil](/molmil-images/mine/4wh1) | N-Acetylhexosamine 1-kinase (ligand free) | Descriptor: | ACETIC ACID, GLYCEROL, N-acetylhexosamine 1-kinase | Authors: | Sato, M, Arakawa, T, Nam, Y.W, Nishimoto, M, Kitaoka, M, Fushinobu, S. | Deposit date: | 2014-09-19 | Release date: | 2015-02-11 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.05 Å) | Cite: | Open-close structural change upon ligand binding and two magnesium ions required for the catalysis of N-acetylhexosamine 1-kinase Biochim.Biophys.Acta, 1854, 2015
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4WH3
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![BU of 4wh3 by Molmil](/molmil-images/mine/4wh3) | N-acetylhexosamine 1-kinase in complex with ATP | Descriptor: | ACETIC ACID, ADENOSINE-5'-TRIPHOSPHATE, GLYCEROL, ... | Authors: | Sato, M, Arakawa, T, Nam, Y.W, Nishimoto, M, Kitaoka, M, Fushinobu, S. | Deposit date: | 2014-09-19 | Release date: | 2015-02-18 | Last modified: | 2020-02-05 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Open-close structural change upon ligand binding and two magnesium ions required for the catalysis of N-acetylhexosamine 1-kinase Biochim.Biophys.Acta, 1854, 2015
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3WFZ
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![BU of 3wfz by Molmil](/molmil-images/mine/3wfz) | Crystal structure of Galacto-N-Biose/Lacto-N-Biose I Phosphorylase C236Y Mutant | Descriptor: | 2-acetamido-2-deoxy-alpha-D-glucopyranose, Lacto-N-biose phosphorylase | Authors: | Koyama, Y, Hidaka, M, Kawakami, M, Nishimoto, M, Kitaoka, M. | Deposit date: | 2013-07-25 | Release date: | 2013-10-09 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Directed evolution to enhance thermostability of galacto-N-biose/lacto-N-biose I phosphorylase. Protein Eng.Des.Sel., 26, 2013
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8IP8
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![BU of 8ip8 by Molmil](/molmil-images/mine/8ip8) | Wheat 80S ribosome stalled on AUG-Stop boron dependently | Descriptor: | 18S ribosomal RNA, 40S ribosomal protein eL8, 40S ribosomal protein eS1, ... | Authors: | Yokoyama, T, Tanaka, M, Saito, H, Nishimoto, M, Tsuda, K, Sotta, N, Shigematsu, H, Shirouzu, M, Iwasaki, S, Ito, T, Fujiwara, T. | Deposit date: | 2023-03-14 | Release date: | 2024-02-21 | Last modified: | 2024-05-15 | Method: | ELECTRON MICROSCOPY (2.9 Å) | Cite: | Boric acid intercepts 80S ribosome migration from AUG-stop by stabilizing eRF1. Nat.Chem.Biol., 20, 2024
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8IPB
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![BU of 8ipb by Molmil](/molmil-images/mine/8ipb) | Wheat 80S ribosome pausing on AUG-Stop with cycloheximide | Descriptor: | 18S ribosomal RNA, 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione, 40S ribosomal protein eL8, ... | Authors: | Yokoyama, T, Tanaka, M, Saito, H, Nishimoto, M, Tsuda, K, Sotta, N, Shigematsu, H, Shirouzu, M, Iwasaki, S, Ito, T, Fujiwara, T. | Deposit date: | 2023-03-14 | Release date: | 2024-02-21 | Last modified: | 2024-05-15 | Method: | ELECTRON MICROSCOPY (3.4 Å) | Cite: | Boric acid intercepts 80S ribosome migration from AUG-stop by stabilizing eRF1. Nat.Chem.Biol., 20, 2024
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8IPA
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![BU of 8ipa by Molmil](/molmil-images/mine/8ipa) | Wheat 80S ribosome stalled on AUG-Stop boron dependently with cycloheximide | Descriptor: | 18S ribosomal RNA, 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione, 40S ribosomal protein eL8, ... | Authors: | Yokoyama, T, Tanaka, M, Saito, H, Nishimoto, M, Tsuda, K, Sotta, N, Shigematsu, H, Shirouzu, M, Iwasaki, S, Ito, T, Fujiwara, T. | Deposit date: | 2023-03-14 | Release date: | 2024-02-21 | Last modified: | 2024-05-15 | Method: | ELECTRON MICROSCOPY (3.4 Å) | Cite: | Boric acid intercepts 80S ribosome migration from AUG-stop by stabilizing eRF1. Nat.Chem.Biol., 20, 2024
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8IP9
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![BU of 8ip9 by Molmil](/molmil-images/mine/8ip9) | Wheat 40S ribosome in complex with a tRNAi | Descriptor: | 18S ribosomal RNA, 40S ribosomal protein S23, 40S ribosomal protein eS1, ... | Authors: | Yokoyama, T, Tanaka, M, Saito, H, Nishimoto, M, Tsuda, K, Sotta, N, Shigematsu, H, Shirouzu, M, Iwasaki, S, Ito, T, Fujiwara, T. | Deposit date: | 2023-03-14 | Release date: | 2024-02-21 | Last modified: | 2024-05-15 | Method: | ELECTRON MICROSCOPY (3 Å) | Cite: | Boric acid intercepts 80S ribosome migration from AUG-stop by stabilizing eRF1. Nat.Chem.Biol., 20, 2024
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2ZUU
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![BU of 2zuu by Molmil](/molmil-images/mine/2zuu) | Crystal structure of Galacto-N-biose/Lacto-N-biose I phosphorylase in complex with GlcNAc | Descriptor: | 2-acetamido-2-deoxy-alpha-D-glucopyranose, GLYCEROL, Lacto-N-biose phosphorylase, ... | Authors: | Hidaka, M, Nishimoto, M, Kitaoka, M, Wakagi, T, Shoun, H, Fushinobu, S. | Deposit date: | 2008-10-28 | Release date: | 2008-12-30 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | The crystal structure of galacto-N-biose/lacto-N-biose I phosphorylase: A large deformation of a tim barrel scaffold J.Biol.Chem., 284, 2009
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2ZUV
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![BU of 2zuv by Molmil](/molmil-images/mine/2zuv) | Crystal structure of Galacto-N-biose/Lacto-N-biose I phosphorylase in complex with GlcNAc, Ethylene glycol, and nitrate | Descriptor: | 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-alpha-D-glucopyranose, Lacto-N-biose phosphorylase, ... | Authors: | Hidaka, M, Nishimoto, M, Kitaoka, M, Wakagi, T, Shoun, H, Fushinobu, S. | Deposit date: | 2008-10-28 | Release date: | 2008-12-30 | Last modified: | 2024-04-03 | Method: | X-RAY DIFFRACTION (1.85 Å) | Cite: | The crystal structure of galacto-N-biose/lacto-N-biose I phosphorylase: A large deformation of a tim barrel scaffold J.Biol.Chem., 284, 2009
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2ZUW
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![BU of 2zuw by Molmil](/molmil-images/mine/2zuw) | Crystal structure of Galacto-N-biose/Lacto-N-biose I phosphorylase in complex with GlcNAc and sulfate | Descriptor: | 2-acetamido-2-deoxy-alpha-D-glucopyranose, GLYCEROL, Lacto-N-biose phosphorylase, ... | Authors: | Hidaka, M, Nishimoto, M, Kitaoka, M, Wakagi, T, Shoun, H, Fushinobu, S. | Deposit date: | 2008-10-28 | Release date: | 2008-12-30 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (2.11 Å) | Cite: | The crystal structure of galacto-N-biose/lacto-N-biose I phosphorylase: A large deformation of a tim barrel scaffold J.Biol.Chem., 284, 2009
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2ZUT
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![BU of 2zut by Molmil](/molmil-images/mine/2zut) | Crystal structure of Galacto-N-biose/Lacto-N-biose I phosphorylase in complex with GalNAc | Descriptor: | 2-acetamido-2-deoxy-alpha-D-galactopyranose, GLYCEROL, Lacto-N-biose phosphorylase, ... | Authors: | Hidaka, M, Nishimoto, M, Kitaoka, M, Wakagi, T, Shoun, H, Fushinobu, S. | Deposit date: | 2008-10-28 | Release date: | 2008-12-30 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | The crystal structure of galacto-N-biose/lacto-N-biose I phosphorylase: A large deformation of a tim barrel scaffold J.Biol.Chem., 284, 2009
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2ZUS
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![BU of 2zus by Molmil](/molmil-images/mine/2zus) | Crystal structure of Galacto-N-biose/Lacto-N-biose I phosphorylase | Descriptor: | Lacto-N-biose phosphorylase, MAGNESIUM ION | Authors: | Hidaka, M, Nishimoto, M, Kitaoka, M, Wakagi, T, Shoun, H, Fushinobu, S. | Deposit date: | 2008-10-28 | Release date: | 2008-12-30 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (2.11 Å) | Cite: | The crystal structure of galacto-N-biose/lacto-N-biose I phosphorylase: A large deformation of a tim barrel scaffold J.Biol.Chem., 284, 2009
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2CZL
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![BU of 2czl by Molmil](/molmil-images/mine/2czl) | Crystal structure of MqnD (TTHA1568), a menaquinone biosynthetic enzyme from Thermus thermophilus HB8 (Cys11 modified with beta-mercaptoethanol) | Descriptor: | 3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL, L(+)-TARTARIC ACID, POTASSIUM ION, ... | Authors: | Arai, R, Nishino, A, Nagano, K, Kamo-Uchikubo, T, Nishimoto, M, Toyama, M, Terada, T, Murayama, K, Shirouzu, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2005-07-13 | Release date: | 2006-01-13 | Last modified: | 2011-07-13 | Method: | X-RAY DIFFRACTION (1.55 Å) | Cite: | Crystal structure of MqnD (TTHA1568), a menaquinone biosynthetic enzyme from Thermus thermophilus HB8. J.Struct.Biol., 168, 2009
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6K0H
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![BU of 6k0h by Molmil](/molmil-images/mine/6k0h) | Crystal Structure of UDP-glucose 4-epimerase from Bifidobacterium longum in complex with NAD+ and UDP-GlcNAc | Descriptor: | DI(HYDROXYETHYL)ETHER, MAGNESIUM ION, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, ... | Authors: | Nam, Y.-W, Nishimoto, M, Arakawa, T, Kitaoka, M, Fushinobu, S. | Deposit date: | 2019-05-06 | Release date: | 2019-08-07 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Structural basis for broad substrate specificity of UDP-glucose 4-epimerase in the human milk oligosaccharide catabolic pathway of Bifidobacterium longum. Sci Rep, 9, 2019
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6K0I
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![BU of 6k0i by Molmil](/molmil-images/mine/6k0i) | Crystal Structure of UDP-glucose 4-epimerase from Bifidobacterium longum in complex with NAD+ and UDP-Glc | Descriptor: | NICOTINAMIDE-ADENINE-DINUCLEOTIDE, UDP-glucose 4-epimerase, URIDINE-5'-DIPHOSPHATE-GLUCOSE | Authors: | Nam, Y.-W, Nishimoto, M, Arakawa, T, Kitaoka, M, Fushinobu, S. | Deposit date: | 2019-05-06 | Release date: | 2019-08-07 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Structural basis for broad substrate specificity of UDP-glucose 4-epimerase in the human milk oligosaccharide catabolic pathway of Bifidobacterium longum. Sci Rep, 9, 2019
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6K0G
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![BU of 6k0g by Molmil](/molmil-images/mine/6k0g) | Crystal Structure of UDP-glucose 4-epimerase from Bifidobacterium longum in complex with NAD+ and UDP | Descriptor: | MAGNESIUM ION, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, UDP-glucose 4-epimerase, ... | Authors: | Nam, Y.-W, Nishimoto, M, Arakawa, T, Kitaoka, M, Fushinobu, S. | Deposit date: | 2019-05-06 | Release date: | 2019-08-07 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Structural basis for broad substrate specificity of UDP-glucose 4-epimerase in the human milk oligosaccharide catabolic pathway of Bifidobacterium longum. Sci Rep, 9, 2019
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3A3U
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![BU of 3a3u by Molmil](/molmil-images/mine/3a3u) | Crystal structure of MqnD (TTHA1568), a menaquinone biosynthetic enzyme from Thermus thermophilus HB8 | Descriptor: | 2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL, L(+)-TARTARIC ACID, Menaquinone biosynthetic enzyme, ... | Authors: | Arai, R, Nishino, A, Nagano, K, Uchikubo-Kamo, T, Katsura, K, Nishimoto, M, Toyama, M, Terada, T, Kuramitsu, S, Murayama, K, Shirouzu, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2009-06-20 | Release date: | 2009-07-14 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.65 Å) | Cite: | Crystal structure of MqnD (TTHA1568), a menaquinone biosynthetic enzyme from Thermus thermophilus HB8. J.Struct.Biol., 168, 2009
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3AWI
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![BU of 3awi by Molmil](/molmil-images/mine/3awi) | Bifunctional tRNA modification enzyme MnmC from Escherichia coli | Descriptor: | FLAVIN-ADENINE DINUCLEOTIDE, SULFATE ION, tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein mnmC | Authors: | Kitamura, A, Sengoku, T, Nishimoto, M, Yokoyama, S, Bessho, Y. | Deposit date: | 2011-03-23 | Release date: | 2011-06-01 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (3 Å) | Cite: | Crystal structure of the bifunctional tRNA modification enzyme MnmC from Escherichia coli Protein Sci., 2011
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1VS3
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![BU of 1vs3 by Molmil](/molmil-images/mine/1vs3) | Crystal Structure of the tRNA Pseudouridine Synthase TruA From Thermus thermophilus HB8 | Descriptor: | tRNA pseudouridine synthase A | Authors: | Dong, X, Bessho, Y, Shirouzu, M, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2006-06-28 | Release date: | 2006-12-12 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (2.25 Å) | Cite: | Crystal structure of tRNA pseudouridine synthase TruA from Thermus thermophilus HB8. Rna Biol., 3, 2006
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6K71
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![BU of 6k71 by Molmil](/molmil-images/mine/6k71) | eIF2 - eIF2B complex | Descriptor: | Eukaryotic translation initiation factor 2 subunit 1, Eukaryotic translation initiation factor 2 subunit 2, Eukaryotic translation initiation factor 2 subunit 3, ... | Authors: | Kashiwagi, K, Yokoyama, T, Ito, T. | Deposit date: | 2019-06-05 | Release date: | 2019-07-10 | Last modified: | 2024-03-27 | Method: | ELECTRON MICROSCOPY (4.3 Å) | Cite: | Structural basis for eIF2B inhibition in integrated stress response. Science, 364, 2019
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7D45
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![BU of 7d45 by Molmil](/molmil-images/mine/7d45) | eIF2B-eIF2(aP), aP1 complex | Descriptor: | Eukaryotic translation initiation factor 2 subunit 1, Translation initiation factor eIF-2B subunit alpha, Translation initiation factor eIF-2B subunit beta, ... | Authors: | Kashiwagi, K, Ito, T. | Deposit date: | 2020-09-22 | Release date: | 2020-12-09 | Last modified: | 2021-01-27 | Method: | ELECTRON MICROSCOPY (3.8 Å) | Cite: | ISRIB Blunts the Integrated Stress Response by Allosterically Antagonising the Inhibitory Effect of Phosphorylated eIF2 on eIF2B. Mol.Cell, 81, 2021
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7D44
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![BU of 7d44 by Molmil](/molmil-images/mine/7d44) | eIF2B-eIF2(aP), aP2 complex | Descriptor: | Eukaryotic translation initiation factor 2 subunit 1, Translation initiation factor eIF-2B subunit alpha, Translation initiation factor eIF-2B subunit beta, ... | Authors: | Kashiwagi, K, Ito, T. | Deposit date: | 2020-09-22 | Release date: | 2020-12-09 | Last modified: | 2021-01-27 | Method: | ELECTRON MICROSCOPY (4 Å) | Cite: | ISRIB Blunts the Integrated Stress Response by Allosterically Antagonising the Inhibitory Effect of Phosphorylated eIF2 on eIF2B. Mol.Cell, 81, 2021
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7D46
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![BU of 7d46 by Molmil](/molmil-images/mine/7d46) | eIF2B apo | Descriptor: | Translation initiation factor eIF-2B subunit alpha, Translation initiation factor eIF-2B subunit beta, Translation initiation factor eIF-2B subunit delta, ... | Authors: | Kashiwagi, K, Ito, T. | Deposit date: | 2020-09-22 | Release date: | 2020-12-09 | Last modified: | 2024-03-27 | Method: | ELECTRON MICROSCOPY (4 Å) | Cite: | ISRIB Blunts the Integrated Stress Response by Allosterically Antagonising the Inhibitory Effect of Phosphorylated eIF2 on eIF2B. Mol.Cell, 81, 2021
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