8JPW
| Crystal Structure of Single-chain L-Glutamate Oxidase Mutant from Streptomyces sp. X-119-6 | Descriptor: | 2-OXOGLUTARIC ACID, FLAVIN-ADENINE DINUCLEOTIDE, L-glutamate oxidase, ... | Authors: | Yamaguchi, H, Takahashi, K, Tatsumi, M, Tagami, U, Mizukoshi, T, Miyano, H, Sugiki, M. | Deposit date: | 2023-06-13 | Release date: | 2023-08-09 | Last modified: | 2024-05-08 | Method: | X-RAY DIFFRACTION (2.66 Å) | Cite: | Development of a novel single-chain l-glutamate oxidase from Streptomyces sp. X-119-6 by inserting flexible linkers. Enzyme.Microb.Technol., 170, 2023
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7WAB
| Crystal structure of the prolyl endoprotease, PEP, from Aspergillus niger | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, COMPASS (Complex proteins associated with Set1p) component shg1 family protein, ... | Authors: | Miyazono, K, Kubota, K, Takahashi, K, Tanokura, M. | Deposit date: | 2021-12-14 | Release date: | 2022-01-12 | Last modified: | 2022-02-16 | Method: | X-RAY DIFFRACTION (1.75 Å) | Cite: | Crystal structure and substrate recognition mechanism of the prolyl endoprotease PEP from Aspergillus niger. Biochem.Biophys.Res.Commun., 591, 2022
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3TRS
| The crystal structure of aspergilloglutamic peptidase from Aspergillus niger | Descriptor: | Aspergillopepsin-2 heavy chain, Aspergillopepsin-2 light chain, DIMETHYL SULFOXIDE | Authors: | Sasaki, H, Kubota, K, Lee, W.C, Ohtsuka, J, Kojima, M, Takahashi, K, Tanokura, M. | Deposit date: | 2011-09-10 | Release date: | 2012-08-22 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.6 Å) | Cite: | The crystal structure of an intermediate dimer of aspergilloglutamic peptidase that mimics the enzyme-activation product complex produced upon autoproteolysis. J.Biochem., 152, 2012
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7ZCJ
| Crystal structure of Pizza6-TNH-TSH with Silicotungstic Acid (STA) polyoxometalate | Descriptor: | Keggin (STA), Pizza6-TNH-TSH | Authors: | Wouters, S.M.L, Kamata, K, Takahashi, K, Vandebroek, L, Parac-Vogt, T.N, Tame, J.R.H, Voet, A.R.D. | Deposit date: | 2022-03-28 | Release date: | 2023-04-19 | Last modified: | 2024-02-07 | Method: | X-RAY DIFFRACTION (1.56 Å) | Cite: | Mutational study of a symmetry matched protein-polyoxometalate interface To be published
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2D19
| Solution RNA structure of loop region of the HIV-1 dimerization initiation site in the kissing-loop dimer | Descriptor: | 5'-R(*GP*CP*UP*GP*AP*AP*GP*UP*GP*CP*AP*CP*AP*CP*GP*GP*C)-3' | Authors: | Baba, S, Takahashi, K, Noguchi, S, Takaku, H, Koyanagi, Y, Yamamoto, N, Kawai, G. | Deposit date: | 2005-08-15 | Release date: | 2005-11-01 | Last modified: | 2022-03-09 | Method: | SOLUTION NMR | Cite: | Solution RNA structures of the HIV-1 dimerization initiation site in the kissing-loop and extended-duplex dimers. J.Biochem.(Tokyo), 138, 2005
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2D17
| Solution RNA structure of stem-bulge-stem region of the HIV-1 dimerization initiation site | Descriptor: | 5'-R(*CP*GP*GP*CP*AP*AP*GP*AP*GP*GP*CP*GP*AP*CP*CP*C)-3', 5'-R(*GP*GP*GP*UP*CP*GP*GP*CP*UP*UP*GP*CP*UP*G)-3' | Authors: | Baba, S, Takahashi, K, Noguchi, S, Takaku, H, Koyanagi, Y, Yamamoto, N, Kawai, G. | Deposit date: | 2005-08-15 | Release date: | 2005-11-01 | Last modified: | 2022-03-09 | Method: | SOLUTION NMR | Cite: | Solution RNA structures of the HIV-1 dimerization initiation site in the kissing-loop and extended-duplex dimers. J.Biochem.(Tokyo), 138, 2005
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2D1A
| Solution RNA structure model of the HIV-1 dimerization initiation site in the extended-duplex dimer | Descriptor: | RNA | Authors: | Baba, S, Takahashi, K, Noguchi, S, Takaku, H, Koyanagi, Y, Yamamoto, N, Kawai, G. | Deposit date: | 2005-08-15 | Release date: | 2005-11-01 | Last modified: | 2022-03-09 | Method: | SOLUTION NMR | Cite: | Solution RNA structures of the HIV-1 dimerization initiation site in the kissing-loop and extended-duplex dimers. J.Biochem.(Tokyo), 138, 2005
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2D18
| Solution RNA structure of loop region of the HIV-1 dimerization initiation site in the extended-duplex dimer | Descriptor: | 5'-R(*GP*CP*UP*GP*AP*AP*GP*UP*GP*CP*AP*CP*AP*CP*GP*GP*C)-3' | Authors: | Baba, S, Takahashi, K, Noguchi, S, Takaku, H, Koyanagi, Y, Yamamoto, N, Kawai, G. | Deposit date: | 2005-08-15 | Release date: | 2005-11-01 | Last modified: | 2022-03-09 | Method: | SOLUTION NMR | Cite: | Solution RNA structures of the HIV-1 dimerization initiation site in the kissing-loop and extended-duplex dimers. J.Biochem.(Tokyo), 138, 2005
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2D1B
| Solution RNA structure model of the HIV-1 dimerization initiation site in the kissing-loop dimer | Descriptor: | RNA | Authors: | Baba, S, Takahashi, K, Noguchi, S, Takaku, H, Koyanagi, Y, Yamamoto, N, Kawai, G. | Deposit date: | 2005-08-15 | Release date: | 2005-11-01 | Last modified: | 2022-03-09 | Method: | SOLUTION NMR | Cite: | Solution RNA structures of the HIV-1 dimerization initiation site in the kissing-loop and extended-duplex dimers. J.Biochem.(Tokyo), 138, 2005
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7VUU
| Crystal structure of AlleyCat10 with inhibitor | Descriptor: | 5-nitro-1H-benzotriazole, AlleyCat, CALCIUM ION | Authors: | Tame, J.R.H, Korendovych, I.V, Margheritis, E, Takahashi, K. | Deposit date: | 2021-11-04 | Release date: | 2022-07-27 | Last modified: | 2022-10-26 | Method: | X-RAY DIFFRACTION (1.95 Å) | Cite: | NMR-guided directed evolution. Nature, 610, 2022
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7VUT
| Crystal structure of AlleyCat10 | Descriptor: | AlleyCat10, CALCIUM ION | Authors: | Tame, J.R.H, Korendovych, I.V, Margheritis, E, Takahashi, K. | Deposit date: | 2021-11-04 | Release date: | 2022-07-27 | Last modified: | 2022-10-26 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | NMR-guided directed evolution. Nature, 610, 2022
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7VUS
| Crystal structure of AlleyCat9 with 5-nitro-benzotriazole | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, 5-nitro-1H-benzotriazole, AlleyCat, ... | Authors: | Tame, J.R.H, Korendovych, I.V, Margheritis, E, Takahashi, K. | Deposit date: | 2021-11-04 | Release date: | 2022-07-27 | Last modified: | 2022-10-26 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | NMR-guided directed evolution. Nature, 610, 2022
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7VUR
| Crystal structure of AlleyCat9 with calcium but no inhibitor | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, AlleyCat, CALCIUM ION | Authors: | Margheritis, E, Takahashi, K, Korendovych, I.V, Tame, J.R.H. | Deposit date: | 2021-11-04 | Release date: | 2022-07-27 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | NMR-guided directed evolution. Nature, 610, 2022
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5ZBD
| Crystal structure of tryptophan oxidase (C395A mutant) from Chromobacterium violaceum | Descriptor: | FLAVIN-ADENINE DINUCLEOTIDE, Flavin-dependent L-tryptophan oxidase VioA, TRYPTOPHAN | Authors: | Yamaguchi, H, Tatsumi, M, Takahashi, K, Tagami, U, Sugiki, M, Kashiwagi, T, Okazaki, S, Mizukoshi, T, Asano, Y. | Deposit date: | 2018-02-11 | Release date: | 2018-12-19 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Protein engineering for improving the thermostability of tryptophan oxidase and insights from structural analysis. J. Biochem., 164, 2018
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5ZBC
| Crystal structure of Se-Met tryptophan oxidase (C395A mutant) from Chromobacterium violaceum | Descriptor: | FLAVIN-ADENINE DINUCLEOTIDE, Flavin-dependent L-tryptophan oxidase VioA | Authors: | Yamaguchi, H, Tatsumi, M, Takahashi, K, Tagami, U, Sugiki, M, Kashiwagi, T, Okazaki, S, Mizukoshi, T, Asano, Y. | Deposit date: | 2018-02-11 | Release date: | 2018-12-19 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Protein engineering for improving the thermostability of tryptophan oxidase and insights from structural analysis. J. Biochem., 164, 2018
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1BI6
| NMR STRUCTURE OF BROMELAIN INHIBITOR VI FROM PINEAPPLE STEM | Descriptor: | BROMELAIN INHIBITOR VI | Authors: | Hatano, K.-I. | Deposit date: | 1995-12-07 | Release date: | 1996-04-03 | Last modified: | 2017-11-29 | Method: | SOLUTION NMR | Cite: | Solution structure of bromelain inhibitor IV from pineapple stem: structural similarity with Bowman-Birk trypsin/chymotrypsin inhibitor from soybean. Biochemistry, 35, 1996
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3SYU
| Re-refined coordinates for pdb entry 1det - ribonuclease T1 carboxymethylated at GLU 58 in complex with 2'GMP | Descriptor: | GUANOSINE-2'-MONOPHOSPHATE, Guanyl-specific ribonuclease T1, SODIUM ION, ... | Authors: | Smart, O.S, Womack, T.O, Bricogne, G. | Deposit date: | 2011-07-18 | Release date: | 2012-03-28 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (1.95 Å) | Cite: | Exploiting structure similarity in refinement: automated NCS and target-structure restraints in BUSTER. Acta Crystallogr.,Sect.D, 68, 2012
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8WGS
| Crystal structure of V30M-TTR in complex with compound 4 | Descriptor: | Transthyretin, [3,5-bis(iodanyl)-4-oxidanyl-phenyl]-(2-ethyl-4-iodanyl-1-benzofuran-3-yl)methanone | Authors: | Yokoyama, T. | Deposit date: | 2023-09-22 | Release date: | 2024-05-15 | Method: | X-RAY DIFFRACTION (1.801 Å) | Cite: | Development of Benziodarone Analogues with Enhanced Potency for Selective Binding to Transthyretin in Human Plasma. J.Med.Chem., 2024
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8WGT
| Crystal structure of V30M-TTR in complex with compound 7 | Descriptor: | Transthyretin, [4,7-bis(chloranyl)-2-ethyl-1-benzofuran-3-yl]-[3,5-bis(iodanyl)-4-oxidanyl-phenyl]methanone | Authors: | Yokoyama, T. | Deposit date: | 2023-09-22 | Release date: | 2024-05-15 | Method: | X-RAY DIFFRACTION (1.696 Å) | Cite: | Development of Benziodarone Analogues with Enhanced Potency for Selective Binding to Transthyretin in Human Plasma. J.Med.Chem., 2024
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8WGU
| Crystal structure of V30M-TTR in complex with compound 20 | Descriptor: | Transthyretin, [3,5-bis(iodanyl)-4-oxidanyl-phenyl]-[2-ethyl-4,7-bis(fluoranyl)-1-benzofuran-3-yl]methanone | Authors: | Yokoyama, T. | Deposit date: | 2023-09-22 | Release date: | 2024-05-15 | Method: | X-RAY DIFFRACTION (1.508 Å) | Cite: | Development of Benziodarone Analogues with Enhanced Potency for Selective Binding to Transthyretin in Human Plasma. J.Med.Chem., 2024
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1VCV
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6LF1
| SeviL, a GM1b/asialo-GM1 binding lectin | Descriptor: | CHLORIDE ION, SeviL | Authors: | Kamata, K, Ozeki, Y, Park, S.-Y, Tame, J.R.H. | Deposit date: | 2019-11-28 | Release date: | 2020-12-02 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | The structure of SeviL, a GM1b/asialo-GM1 binding R-type lectin from the mussel Mytilisepta virgata. Sci Rep, 10, 2020
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6LF2
| SeviL bound to asialo-GM1 saccharide | Descriptor: | SeviL, beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose | Authors: | Kamata, K, Ozeki, Y, Park, S.-Y, Tame, J.R.H. | Deposit date: | 2019-11-28 | Release date: | 2020-12-02 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.6 Å) | Cite: | The structure of SeviL, a GM1b/asialo-GM1 binding R-type lectin from the mussel Mytilisepta virgata. Sci Rep, 10, 2020
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4ZY3
| Crystal Structure of Keap1 in Complex with a small chemical compound, K67 | Descriptor: | FORMIC ACID, Kelch-like ECH-associated protein 1, N,N'-[2-(2-oxopropyl)naphthalene-1,4-diyl]bis(4-ethoxybenzenesulfonamide) | Authors: | Fukutomi, T, Iso, T, Suzuki, T, Takagi, K, Mizushima, T, Komatsu, M, Yamamoto, M. | Deposit date: | 2015-05-21 | Release date: | 2016-05-25 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | p62/Sqstm1 promotes malignancy of HCV-positive hepatocellular carcinoma through Nrf2-dependent metabolic reprogramming Nat Commun, 7, 2016
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2BI6
| NMR STUDY OF BROMELAIN INHIBITOR VI FROM PINEAPPLE STEM | Descriptor: | BROMELAIN INHIBITOR VI | Authors: | Hatano, K.-I. | Deposit date: | 1995-12-07 | Release date: | 1996-04-03 | Last modified: | 2017-11-29 | Method: | SOLUTION NMR | Cite: | Solution structure of bromelain inhibitor IV from pineapple stem: structural similarity with Bowman-Birk trypsin/chymotrypsin inhibitor from soybean. Biochemistry, 35, 1996
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