6B8A
| Crystal structure of MvfR ligand binding domain in complex with M64 | Descriptor: | 2-[(5-nitro-1H-benzimidazol-2-yl)sulfanyl]-N-(4-phenoxyphenyl)acetamide, COBALT HEXAMMINE(III), DNA-binding transcriptional regulator | Authors: | Kitao, T, Steinbacher, S, Maskos, K, Blaesse, M, Rahme, L.G. | Deposit date: | 2017-10-05 | Release date: | 2018-01-31 | Last modified: | 2023-10-04 | Method: | X-RAY DIFFRACTION (2.65 Å) | Cite: | Molecular Insights into Function and Competitive Inhibition ofPseudomonas aeruginosaMultiple Virulence Factor Regulator. MBio, 9, 2018
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2D2I
| Crystal Structure of NADP-Dependent Glyceraldehyde-3-Phosphate Dehydrogenase from Synechococcus Sp. complexed with Nadp+ | Descriptor: | NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, SULFATE ION, glyceraldehyde 3-phosphate dehydrogenase | Authors: | Kitatani, T, Nakamura, Y, Wada, K, Kinoshita, T, Tamoi, M, Shigeoka, S, Tada, T. | Deposit date: | 2005-09-09 | Release date: | 2006-07-11 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Structure of NADP-dependent glyceraldehyde-3-phosphate dehydrogenase from Synechococcus PCC7942 complexed with NADP Acta Crystallogr.,Sect.F, 62, 2006
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2DUU
| Crystal Structure of apo-form of NADP-Dependent Glyceraldehyde-3-Phosphate Dehydrogenase from Synechococcus Sp. | Descriptor: | Glyceraldehyde 3-phosphate dehydrogenase, SULFATE ION | Authors: | Kitatani, T, Nakamura, Y, Wada, K, Kinoshita, T, Tamoi, M, Shigeoka, S, Tada, T. | Deposit date: | 2006-07-27 | Release date: | 2006-09-05 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.9 Å) | Cite: | Structure of apo-glyceraldehyde-3-phosphate dehydrogenase from Synechococcus PCC7942 Acta Crystallogr.,Sect.F, 62, 2006
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7C9J
| Transglutaminase from Geobacillus stearothermophilus (without C-terminal extension) | Descriptor: | 1,2-ETHANEDIOL, CITRIC ACID, Protein-glutamine gamma-glutamyltransferase | Authors: | Takita, T, Mikami, B, Lei, Y, Jing, Y, Yamada, A, Yasukawa, K. | Deposit date: | 2020-06-06 | Release date: | 2021-06-09 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Transglutaminase from Geobacillus stearothermophilus (without C-terminal extension) To be published
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2Z6E
| Crystal Structure of Human DAAM1 FH2 | Descriptor: | Disheveled-associated activator of morphogenesis 1 | Authors: | Yamashita, M, Higashi, T, Sato, Y, Shirakawa, R, Kita, T, Horiuchi, H, Fukai, S, Nureki, O. | Deposit date: | 2007-07-31 | Release date: | 2008-05-27 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Crystal structure of human DAAM1 formin homology 2 domain Genes Cells, 12, 2007
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8Y1M
| Xylanase R from Bacillus sp. TAR-1 complexed with xylobiose. | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, ACETATE ION, ... | Authors: | Nakamura, T, Kuwata, K, Takita, T, Mizutani, K, Mikami, B, Nakamura, S, Yasukawa, K. | Deposit date: | 2024-01-25 | Release date: | 2024-05-22 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Activity-stability trade-off observed in variants at position 315 of the GH10 xylanase XynR. Sci Rep, 14, 2024
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8XY0
| Activity-stability trade-off observed in variants at position 315 of the GH10 xylanase XynR | Descriptor: | CALCIUM ION, DI(HYDROXYETHYL)ETHER, Endo-1,4-beta-xylanase A | Authors: | Nakamura, T, Takita, T, Mizutani, K, Mikami, B, Nakamura, S, Yasukawa, K. | Deposit date: | 2024-01-19 | Release date: | 2024-05-22 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | Activity-stability trade-off observed in variants at position 315 of the GH10 xylanase XynR. Sci Rep, 14, 2024
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3H7G
| Apo-FR with AU ions | Descriptor: | CADMIUM ION, Ferritin light chain, GLYCEROL, ... | Authors: | Abe, M, Ueno, T, Abe, S, Suzuki, M, Goto, T, Toda, Y, Akita, T, Yamada, Y, Watanabe, Y. | Deposit date: | 2009-04-27 | Release date: | 2009-09-15 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.65 Å) | Cite: | Preparation and catalytic reaction of Au/Pd bimetallic nanoparticles in apo-ferritin Chem.Commun.(Camb.), 32, 2009
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3IYO
| Cryo-EM model of virion-sized HEV virion-sized capsid | Descriptor: | Capsid protein | Authors: | Xing, L, Mayazaki, N, Li, T.C, Simons, M.N, Wall, J.S, Moore, M, Wang, C.Y, Takeda, N, Wakita, T, Miyamura, T, Cheng, R.H. | Deposit date: | 2010-03-19 | Release date: | 2010-08-18 | Last modified: | 2024-02-21 | Method: | ELECTRON MICROSCOPY (10.5 Å) | Cite: | Structural basis for the RNA-dependent assembly pathway of hepatitis E virion-sized particles J.Biol.Chem., 2010
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3E9I
| Lysyl-tRNA synthetase from Bacillus stearothermophilus complexed with L-Lysine hydroxamate-AMP | Descriptor: | 5'-O-{(R)-hydroxy[(L-lysylamino)oxy]phosphoryl}adenosine, Lysyl-tRNA synthetase, MAGNESIUM ION, ... | Authors: | Sakurama, H, Takita, T, Mikami, B, Itoh, T, Yasukawa, K, Inouye, K. | Deposit date: | 2008-08-22 | Release date: | 2009-07-14 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Two crystal structures of lysyl-tRNA synthetase from Bacillus stearothermophilus in complex with lysyladenylate-like compounds: insights into the irreversible formation of the enzyme-bound adenylate of L-lysine hydroxamate J.Biochem., 145, 2009
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7WSS
| Collagenase from Grimontia (Vibrio) hollisae 1706B | Descriptor: | 1,2-ETHANEDIOL, CALCIUM ION, DI(HYDROXYETHYL)ETHER, ... | Authors: | Ikeuchi, T, Yasumoto, M, Takita, T, Mizutani, K, Mikami, B, Tanaka, K, Hattori, S, Yasukawa, K. | Deposit date: | 2022-02-01 | Release date: | 2022-06-29 | Last modified: | 2024-04-03 | Method: | X-RAY DIFFRACTION (2.19 Å) | Cite: | Crystal structure of Grimontia hollisae collagenase provides insights into its novel substrate specificity toward collagen. J.Biol.Chem., 298, 2022
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7XEB
| Collagenase from Grimontia (Vibrio) hollisae 1706B complexed with Gly-Pro-Hyp | Descriptor: | 1,2-ETHANEDIOL, CALCIUM ION, GLY-PRO-HYP peptide, ... | Authors: | Ikeuchi, T, Yasumoto, M, Takita, T, Mizutani, K, Mikami, B, Tanaka, K, Hattori, S, Yasukawa, K. | Deposit date: | 2022-03-30 | Release date: | 2022-06-29 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.39 Å) | Cite: | Crystal structure of Grimontia hollisae collagenase provides insights into its novel substrate specificity toward collagen. J.Biol.Chem., 298, 2022
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8JT1
| COLLAGENASE FROM GRIMONTIA (VIBRIO) HOLLISAE 1706B COMPLEXED WITH GLY-PRO-HYP-GLY-PRO-HYP | Descriptor: | 1,2-ETHANEDIOL, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 6-mer peptide, ... | Authors: | Ueshima, S, Yaskawa, K, Takita, T, Mikami, B. | Deposit date: | 2023-06-21 | Release date: | 2024-02-07 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Insights into the catalytic mechanism of Grimontia hollisae collagenase through structural and mutational analyses. Febs Lett., 597, 2023
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5C2K
| Crystal structure of the fusion protein linked by RhoA and the GAP domain of MgcRacGAP | Descriptor: | ALUMINUM FLUORIDE, GUANOSINE-5'-DIPHOSPHATE, MAGNESIUM ION, ... | Authors: | Murayama, K, Kato-Murayama, M, Hosaka, T, Kitamura, T, Yokoyama, S, Shirouzu, M. | Deposit date: | 2015-06-16 | Release date: | 2016-06-22 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.42 Å) | Cite: | Structural basis of G-protein target alternation of MgcRacGAP by phospholylation To Be Published
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3E9H
| Lysyl-tRNA synthetase from Bacillus stearothermophilus complexed with L-Lysylsulfamoyl adenosine | Descriptor: | 5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE, Lysyl-tRNA synthetase, MAGNESIUM ION | Authors: | Sakurama, H, Takita, T, Mikami, B, Itoh, T, Yasukawa, K, Inouye, K. | Deposit date: | 2008-08-22 | Release date: | 2009-07-14 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Two crystal structures of lysyl-tRNA synthetase from Bacillus stearothermophilus in complex with lysyladenylate-like compounds: insights into the irreversible formation of the enzyme-bound adenylate of L-lysine hydroxamate J.Biochem., 145, 2009
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1WUN
| Human Factor Viia-Tissue Factor Complexed with ethylsulfonamide-D-Trp-Gln-p-aminobenzamidine | Descriptor: | CALCIUM ION, Coagulation factor VII, N-(ETHYLSULFONYL)TRYPTOPHYL-N~1~-{4-[AMINO(IMINO)METHYL]BENZYL}GLUTAMAMIDE, ... | Authors: | Kadono, S, Sakamoto, A, Kikuchi, Y, Oh-eda, M, Yabuta, N, Yoshihashi, K, Kitazawa, T, Suzuki, T, Koga, T, Hattori, K, Shiraishi, T, Haramura, M, Kodama, H, Ono, Y, Esaki, T, Sato, H, Watanabe, Y, Itoh, S, Ohta, M, Kozono, T. | Deposit date: | 2004-12-08 | Release date: | 2005-12-08 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Structure-based design of P3 moieties in the peptide mimetic factor VIIa inhibitor Biochem.Biophys.Res.Commun., 327, 2005
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5C2J
| Complex structure of the GAP domain of MgcRacGAP and Cdc42 | Descriptor: | ALUMINUM FLUORIDE, Cell division control protein 42 homolog, GUANOSINE-5'-DIPHOSPHATE, ... | Authors: | Murayama, K, Kato-Murayama, M, Hosaka, T, Kitamura, T, Yokoyama, S, Shirouzu, M. | Deposit date: | 2015-06-16 | Release date: | 2016-06-22 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Structural basis of G-protein target alternation of MgcRacGAP by phospholylation To Be Published
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1WV7
| Human Factor Viia-Tissue Factor Complexed with ethylsulfonamide-D-5-propoxy-Trp-Gln-p-aminobenzamidine | Descriptor: | CALCIUM ION, Coagulation factor VII, N-(ETHYLSULFONYL)-5-PROPOXY-L-TRYPTOPHYL-N~1~-{4-[AMINO(IMINO)METHYL]BENZYL}-L-GLUTAMAMIDE, ... | Authors: | Kadono, S, Sakamoto, A, Kikuchi, Y, Oh-eda, M, Yabuta, N, Yoshihashi, K, Kitazawa, T, Suzuki, T, Koga, T, Hattori, K, Shiraishi, T, Haramura, M, Kodama, H, Ono, Y, Esaki, T, Sato, H, Watanabe, Y, Itoh, S, Ohta, M, Kozono, T. | Deposit date: | 2004-12-11 | Release date: | 2005-12-11 | Last modified: | 2020-07-29 | Method: | X-RAY DIFFRACTION (2.7 Å) | Cite: | Structure-based design of P3 moieties in the peptide mimetic factor VIIa inhibitor Biochem.Biophys.Res.Commun., 327, 2005
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1VBL
| Structure of the thermostable pectate lyase PL 47 | Descriptor: | CALCIUM ION, pectate lyase 47 | Authors: | Nakaniwa, T, Tada, T, Yamaguchi, A, Kitatani, T, Takao, M, Sakai, T, Nishimura, K. | Deposit date: | 2004-02-27 | Release date: | 2005-04-19 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (1.91 Å) | Cite: | Structural Basis for Thermostability of Pectate Lyase from Bacillus sp. TS 47 To be Published
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170D
| SOLUTION STRUCTURE OF A DNA DODECAMER CONTAINING THE ANTI-NEOPLASTIC AGENT ARABINOSYLCYTOSINE: COMBINED USE OF NMR, RESTRAINED MOLECULAR DYNAMICS AND FULL RELAXATION MATRIX REFINEMENT | Descriptor: | DNA/RNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*T)-R(P*CAR)-D(P*GP*CP*G)-3') | Authors: | Schweitzer, B.I, Mikita, T, Kellogg, G.W, Gardner, K.H, Beardsley, G.P. | Deposit date: | 1994-03-14 | Release date: | 1994-07-31 | Last modified: | 2024-05-22 | Method: | SOLUTION NMR | Cite: | Solution structure of a DNA dodecamer containing the anti-neoplastic agent arabinosylcytosine: combined use of NMR, restrained molecular dynamics, and full relaxation matrix refinement. Biochemistry, 33, 1994
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7FCI
| human NTCP in complex with YN69083 Fab | Descriptor: | Fab Heavy chain, Fab Light chain, Sodium/bile acid cotransporter | Authors: | Park, J.H, Iwamoto, M, Yun, J.H, Uchikubo-Kamo, T, Son, D, Jin, Z, Yoshida, H, Ohki, M, Ishimoto, N, Mizutani, K, Oshima, M, Muramatsu, M, Wakita, T, Shirouzu, M, Liu, K, Uemura, T, Nomura, N, Iwata, S, Watashi, K, Tame, J.R.H, Nishizawa, T, Lee, W, Park, S.Y. | Deposit date: | 2021-07-14 | Release date: | 2022-05-25 | Last modified: | 2022-07-13 | Method: | ELECTRON MICROSCOPY (3.3 Å) | Cite: | Structural insights into the HBV receptor and bile acid transporter NTCP. Nature, 606, 2022
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1WL7
| Structure of the thermostable arabinanase | Descriptor: | CALCIUM ION, arabinanase-TS | Authors: | Yamaguchi, A, Tada, T, Nakaniwa, T, Kitatani, T. | Deposit date: | 2004-06-21 | Release date: | 2005-06-21 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | Structural basis for thermostability of endo-1,5-alpha-L-arabinanase from Bacillus thermodenitrificans TS-3. J.Biochem.(Tokyo), 137, 2005
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1V9A
| Crystal structure of Uroporphyrin-III C-methyl transferase from Thermus thermophilus complexed with S-adenyl homocysteine | Descriptor: | CITRATE ANION, S-ADENOSYL-L-HOMOCYSTEINE, Uroporphyrin-III C-methyltransferase | Authors: | Rehse, P.H, Kitao, T, Tahirov, T.H, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2004-01-23 | Release date: | 2005-02-01 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Structure of a closed-form uroporphyrinogen-III C-methyltransferase from Thermus thermophilus. Acta Crystallogr.,Sect.D, 61, 2005
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1VA0
| Crystal Structure of the Native Form of Uroporphyrin III C-methyl transferase from Thermus thermophilus | Descriptor: | 1,2-ETHANEDIOL, CHLORIDE ION, Uroporphyrin-III C-methyltransferase | Authors: | Rehse, P.H, Kitao, T, Tahirov, T.H, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2004-02-05 | Release date: | 2005-02-15 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.97 Å) | Cite: | Structure of a closed-form uroporphyrinogen-III C-methyltransferase from Thermus thermophilus. Acta Crystallogr.,Sect.D, 61, 2005
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9JER
| Arginine decarboxylase in Aspergillus oryzae, ligand-free form | Descriptor: | 1,2-ETHANEDIOL, DI(HYDROXYETHYL)ETHER, L-tryptophan decarboxylase PsiD-like domain-containing protein | Authors: | Mikami, B, Yasukawa, K, Fujiwara, S, Takita, T, Mizutani, K, Odagaki, Y, Murakami, Y. | Deposit date: | 2024-09-03 | Release date: | 2024-10-09 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | Unveiling the reaction mechanism of arginine decarboxylase in Aspergillus oryzae: Insights from crystal structure analysis. Biochem.Biophys.Res.Commun., 733, 2024
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