8WM0
 
 | | Crystal structure of TNIK-thiopeptide wTP3 complex | | Descriptor: | ADENOSINE, THIOPEPTIDE wTP3, TRAF2 and NCK-interacting protein kinase | | Authors: | Hamada, K, Kobayashi, S, Vinogradov, A.A, Zhang, Y, Goto, Y, Suga, H, Ogata, K, Sengoku, T. | | Deposit date: | 2023-10-01 | | Release date: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | A Compact Reprogrammed Genetic Code for De Novo Discovery of Proteolytically Stable Thiopeptides.
J.Am.Chem.Soc., 2024
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7VMW
 | | Crystal structure of LimF prenyltransferase bound with a peptide substrate and GSPP | | Descriptor: | GERANYL S-THIOLODIPHOSPHATE, LynF/TruF/PatF family peptide O-prenyltransferase, MAGNESIUM ION, ... | | Authors: | Hamada, K, Kobayashi, S, Okada, C, Zhang, Y, Inoue, S, Goto, Y, Suga, H, Ogata, K, Sengoku, T. | | Deposit date: | 2021-10-09 | | Release date: | 2022-08-03 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.93 Å) | | Cite: | LimF is a versatile prenyltransferase for histidine-C-geranylation on diverse non-natural substrates
Nat Catal, 2022
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7VMY
 | | Crystal structure of LimF prenyltransferase bound with GSPP | | Descriptor: | 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, GERANYL S-THIOLODIPHOSPHATE, LynF/TruF/PatF family peptide O-prenyltransferase, ... | | Authors: | Hamada, K, Kobayashi, S, Okada, C, Zhang, Y, Inoue, S, Goto, Y, Suga, H, Ogata, K, Sengoku, T. | | Deposit date: | 2021-10-09 | | Release date: | 2022-08-03 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.77 Å) | | Cite: | LimF is a versatile prenyltransferase for histidine-C-geranylation on diverse non-natural substrates
Nat Catal, 2022
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1G4F
 | | NMR STRUCTURE OF THE FIFTH DOMAIN OF HUMAN BETA2-GLYCOPROTEIN I | | Descriptor: | BETA2-GLYCOPROTEIN I | | Authors: | Hoshino, M, Hagihara, Y, Nishii, I, Yamazaki, T, Kato, H, Goto, Y. | | Deposit date: | 2000-10-27 | | Release date: | 2000-11-15 | | Last modified: | 2022-02-23 | | Method: | SOLUTION NMR | | Cite: | Identification of the phospholipid-binding site of human beta(2)-glycoprotein I domain V by heteronuclear magnetic resonance.
J.Mol.Biol., 304, 2000
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1G4G
 | | NMR STRUCTURE OF THE FIFTH DOMAIN OF HUMAN BETA2-GLYCOPROTEIN I | | Descriptor: | BETA2-GLYCOPROTEIN I | | Authors: | Hoshino, M, Hagihara, Y, Nishii, I, Yamazaki, T, Kato, H, Goto, Y. | | Deposit date: | 2000-10-27 | | Release date: | 2000-11-15 | | Last modified: | 2022-02-23 | | Method: | SOLUTION NMR | | Cite: | Identification of the phospholipid-binding site of human beta(2)-glycoprotein I domain V by heteronuclear magnetic resonance.
J.Mol.Biol., 304, 2000
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8JE4
 | | Crystal structure of LimF prenyltransferase (H239G/W273T mutant) bound with the thiodiphosphate moiety of farnesyl S-thiolodiphosphate (FSPP) | | Descriptor: | MAGNESIUM ION, TRIHYDROGEN THIODIPHOSPHATE, prenyltransferase, ... | | Authors: | Hamada, K, Oguni, A, Zhang, Y, Satake, M, Goto, Y, Suga, H, Ogata, K, Sengoku, T. | | Deposit date: | 2023-05-15 | | Release date: | 2023-11-08 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.19 Å) | | Cite: | Switching Prenyl Donor Specificities of Cyanobactin Prenyltransferases.
J.Am.Chem.Soc., 145, 2023
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1CJ5
 | | BOVINE BETA-LACTOGLOBULIN A | | Descriptor: | BETA-LACTOGLOBULIN A | | Authors: | Kuwata, K, Hoshino, M, Forge, V, Era, S, Batt, C.A, Goto, Y. | | Deposit date: | 1999-04-22 | | Release date: | 2000-04-26 | | Last modified: | 2023-12-27 | | Method: | SOLUTION NMR | | Cite: | Solution structure and dynamics of bovine beta-lactoglobulin A.
Protein Sci., 8, 1999
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2QY0
 | | Active dimeric structure of the catalytic domain of C1r reveals enzyme-product like contacts | | Descriptor: | Complement C1r subcomponent, GLYCEROL | | Authors: | Kardos, J, Harmat, V, Pallo, A, Barabas, O, Szilagyi, K, Graf, L, Naray-Szabo, G, Goto, Y, Zavodszky, P, Gal, P. | | Deposit date: | 2007-08-13 | | Release date: | 2008-02-05 | | Last modified: | 2023-08-30 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Revisiting the mechanism of the autoactivation of the complement protease C1r in the C1 complex: Structure of the active catalytic region of C1r.
Mol.Immunol., 45, 2008
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6M1B
 | | A new V27M variant of beta 2 microglobulin induced amyloidosis in a patient with long-term hemodialysis | | Descriptor: | Beta-2-microglobulin, CALCIUM ION, GLYCEROL, ... | | Authors: | So, M, Nakahara, S, Nakaniwa, T, Tanaka, H, Kurisu, G, Goto, Y. | | Deposit date: | 2020-02-25 | | Release date: | 2021-01-06 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.88 Å) | | Cite: | Dialysis-related amyloidosis associated with a novel beta 2 -microglobulin variant.
Amyloid, 28, 2021
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3AXG
 | | Structure of 6-aminohexanoate-oligomer hydrolase | | Descriptor: | Endotype 6-aminohexanoat-oligomer hydrolase, SODIUM ION | | Authors: | Negoro, S, Shibata, N, Tanaka, Y, Yasuhira, K, Shibata, H, Hashimoto, H, Lee, Y.H, Ohshima, S, Santa, R, Mochiji, K, Goto, Y, Ikegami, T, Nagai, K, Kato, D, Takeo, M, Higuchi, Y. | | Deposit date: | 2011-04-04 | | Release date: | 2011-12-21 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Three-dimensional structure of nylon hydrolase and mechanism of nylon-6 hydrolysis
J.Biol.Chem., 287, 2012
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7XZQ
 | | Crystal structure of TNIK-thiopeptide TP1 complex | | Descriptor: | 1,4-BUTANEDIOL, TRAF2 and NCK-interacting protein kinase, thiopeptide TP1 | | Authors: | Hamada, K, Vinogradov, A.A, Zhang, Y, Chang, J.S, Nishimura, H, Goto, Y, Onaka, H, Suga, H, Ogata, K, Sengoku, T. | | Deposit date: | 2022-06-03 | | Release date: | 2022-10-26 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.09 Å) | | Cite: | De Novo Discovery of Thiopeptide Pseudo-natural Products Acting as Potent and Selective TNIK Kinase Inhibitors.
J.Am.Chem.Soc., 144, 2022
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7XZR
 | | Crystal structure of TNIK-AMPPNP-thiopeptide TP15 complex | | Descriptor: | MAGNESIUM ION, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, SULFATE ION, ... | | Authors: | Hamada, K, Vinogradov, A.A, Zhang, Y, Chang, J.S, Nishimura, H, Goto, Y, Onaka, H, Suga, H, Ogata, K, Sengoku, T. | | Deposit date: | 2022-06-03 | | Release date: | 2022-10-26 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.26 Å) | | Cite: | De Novo Discovery of Thiopeptide Pseudo-natural Products Acting as Potent and Selective TNIK Kinase Inhibitors.
J.Am.Chem.Soc., 144, 2022
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2YXF
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1WDY
 | | Crystal structure of ribonuclease | | Descriptor: | 2-5A-dependent ribonuclease, 5'-O-MONOPHOSPHORYLADENYLYL(2'->5')ADENYLYL(2'->5')ADENOSINE | | Authors: | Tanaka, N, Nakanishi, M, Kusakabe, Y, Goto, Y, Kitade, Y, Nakamura, K.T. | | Deposit date: | 2004-05-19 | | Release date: | 2004-10-05 | | Last modified: | 2021-11-10 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Structural basis for recognition of 2',5'-linked oligoadenylates by human ribonuclease L
Embo J., 23, 2004
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1X26
 | | Solution structure of the AA-mismatch DNA complexed with naphthyridine-azaquinolone | | Descriptor: | 5'-D(*CP*AP*TP*TP*CP*AP*GP*TP*TP*AP*G)-3', 5'-D(*CP*TP*AP*AP*CP*AP*GP*AP*AP*TP*G)-3', N~3~-{3-[(7-METHYL-1,8-NAPHTHYRIDIN-2-YL)AMINO]-3-OXOPROPYL}-N~1~-[(7-OXO-7,8-DIHYDRO-1,8-NAPHTHYRIDIN-2-YL)METHYL]-BET A-ALANINAMIDE | | Authors: | Nakatani, K, Hagihara, S, Goto, Y, Kobori, A, Hagihara, M, Hayashi, G, Kyo, M, Nomura, M, Mishima, M, Kojima, C. | | Deposit date: | 2005-04-20 | | Release date: | 2006-04-04 | | Last modified: | 2022-03-02 | | Method: | SOLUTION NMR | | Cite: | Small-molecule ligand induces nucleotide flipping in (CAG)n trinucleotide repeats
Nat.Chem.Biol., 1, 2005
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2D4F
 | | The Crystal Structure of human beta2-microglobulin | | Descriptor: | Beta-2-microglobulin, SODIUM ION | | Authors: | Iwata, K, Matsuura, T, Nakagawa, A, Goto, Y. | | Deposit date: | 2005-10-18 | | Release date: | 2006-08-08 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Conformation of Amyloid Fibrils of beta2-Microglobulin Probed by Tryptophan Mutagenesis
J.Biol.Chem., 281, 2006
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2D4D
 | | The Crystal Structure of human beta2-microglobulin, L39W W60F W95F Mutant | | Descriptor: | Beta-2-microglobulin, SODIUM ION | | Authors: | Iwata, K, Matsuura, T, Nakagawa, A, Goto, Y. | | Deposit date: | 2005-10-17 | | Release date: | 2006-08-08 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Conformation of Amyloid Fibrils of beta2-Microglobulin Probed by Tryptophan Mutagenesis
J.Biol.Chem., 281, 2006
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5GVS
 | | Crystal structure of the DDX41 DEAD domain in an apo open form | | Descriptor: | Probable ATP-dependent RNA helicase DDX41 | | Authors: | Omura, H, Oikawa, D, Nakane, T, Kato, M, Ishii, R, Goto, Y, Suga, H, Ishitani, R, Tokunaga, F, Nureki, O. | | Deposit date: | 2016-09-06 | | Release date: | 2016-10-19 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Structural and Functional Analysis of DDX41: a bispecific immune receptor for DNA and cyclic dinucleotide
Sci Rep, 6, 2016
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5GVR
 | | Crystal structure of the DDX41 DEAD domain in an apo closed form | | Descriptor: | (2S)-2-hydroxybutanedioic acid, Probable ATP-dependent RNA helicase DDX41 | | Authors: | Omura, H, Oikawa, D, Nakane, T, Kato, M, Ishii, R, Goto, Y, Suga, H, Ishitani, R, Tokunaga, F, Nureki, O. | | Deposit date: | 2016-09-06 | | Release date: | 2016-10-19 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Structural and Functional Analysis of DDX41: a bispecific immune receptor for DNA and cyclic dinucleotide
Sci Rep, 6, 2016
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