5EXV
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5DCV
| Crystal structure of PhoRpp38-SL12M complex | Descriptor: | 50S ribosomal protein L7Ae, RNA (47-MER) | Authors: | Oshima, K, Tanaka, Y, Yao, M. | Deposit date: | 2015-08-24 | Release date: | 2016-07-06 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (3.401 Å) | Cite: | Structural basis for recognition of a kink-turn motif by an archaeal homologue of human RNase P protein Rpp38 Biochem.Biophys.Res.Commun., 474, 2016
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2EK2
| Structural study of Project ID PH0725 from Pyrococcus horikoshii OT3 (E140M) | Descriptor: | S-ADENOSYL-L-HOMOCYSTEINE, SODIUM ION, diphthine synthase | Authors: | Asada, Y, Matsuura, Y, Tanaka, Y, Nakamoto, T, Kunishima, N, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2007-03-22 | Release date: | 2007-09-25 | Last modified: | 2021-11-10 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Structural study of Project ID PH0725 from Pyrococcus horikoshii OT3 (E140M) To be Published
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2EKB
| Structural study of Project ID TTHB049 from Thermus thermophilus HB8 (L19M) | Descriptor: | Alpha-ribazole-5'-phosphate phosphatase, SODIUM ION | Authors: | Asada, Y, Taketa, M, Tanaka, Y, Matsuura, Y, Kunishima, N, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2007-03-22 | Release date: | 2007-09-25 | Last modified: | 2021-11-10 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Structural study of Project ID TTHB049 from Thermus thermophilus HB8 (L19M) To be Published
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2E8H
| Crystal structure of PH0725 from Pyrococcus horikoshii OT3 | Descriptor: | Probable diphthine synthase, S-ADENOSYL-L-HOMOCYSTEINE, SODIUM ION | Authors: | Sugahara, M, Taketa, M, Tanaka, Y, Matsuura, Y, Kunishima, N, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2007-01-19 | Release date: | 2007-07-24 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Crystal structure of PH0725 from Pyrococcus horikoshii OT3 To be Published
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2E27
| Crystal structure of Fv fragment of anti-ciguatoxin antibody complexed with ABC-ring of ciguatoxin | Descriptor: | 3,7:6,10:9,14-TRIANHYDRO-2,5,11,12,13-PENTADEOXY-4-O-(METHOXYMETHYL)-L-ARABINO-L-ALLO-TETRADEC-12-ENONIC ACID, DIMETHYL SULFOXIDE, GLYCEROL, ... | Authors: | Yokota, A, Tanaka, Y, Tsumoto, K. | Deposit date: | 2006-11-08 | Release date: | 2007-11-13 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Critical contribution of aromatic rings to specific recognition of polyether rings. The case of ciguatoxin CTX3C-ABC and its specific antibody 1C49. J.Biol.Chem., 283, 2008
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2ND5
| Lysine dimethylated FKBP12 | Descriptor: | Peptidyl-prolyl cis-trans isomerase FKBP1A | Authors: | Hattori, Y, Sebera, J, Sychrovsky, V, Furuita, K, Sugiki, T, Ohki, I, Ikegami, T, Kobayashi, N, Tanaka, Y, Fujiwara, T, Kojima, C. | Deposit date: | 2016-05-05 | Release date: | 2017-05-17 | Method: | SOLUTION NMR | Cite: | NMR Observation of Protein Surface Salt Bridges at Neutral pH To be Published
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2OWG
| Crystal structure of PH0725 from Pyrococcus horikoshii OT3 | Descriptor: | S-ADENOSYL-L-HOMOCYSTEINE, SODIUM ION, diphthine synthase | Authors: | Sugahara, M, Matsuura, Y, Tanaka, Y, Nakamoto, T, Kunishima, N, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2007-02-16 | Release date: | 2007-08-21 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Crystal structure of PH0725 from Pyrococcus horikoshii OT3 To be Published
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2PA0
| Crystal structure of TTHB049 from Thermus thermophilus HB8 | Descriptor: | Alpha-ribazole-5'-phosphate phosphatase, CHLORIDE ION, GLYCEROL, ... | Authors: | Sugahara, M, Tanaka, Y, Matsuura, Y, Nakamoto, T, Kunishima, N, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2007-03-27 | Release date: | 2007-10-02 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Crystal structure of TTHB049 from Thermus thermophilus HB8 To be Published
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2P75
| Crystal structure of TTHB049 from Thermus thermophilus HB8 | Descriptor: | Alpha-ribazole-5'-phosphate phosphatase, GLYCEROL, SODIUM ION | Authors: | Sugahara, M, Tanaka, Y, Matsuura, Y, Nakamoto, T, Kunishima, N, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2007-03-20 | Release date: | 2007-09-25 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Crystal structure of TTHB049 from Thermus thermophilus HB8 To be Published
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2P9Z
| Crystal structure of TTHB049 from Thermus thermophilus HB8 | Descriptor: | Alpha-ribazole-5'-phosphate phosphatase, GLYCEROL, SODIUM ION | Authors: | Sugahara, M, Taketa, M, Tanaka, Y, Matsuura, Y, Kunishima, N, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2007-03-26 | Release date: | 2007-10-02 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Crystal structure of TTHB049 from Thermus thermophilus HB8 To be Published
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2P2Z
| Crystal structure of TTHB049 from Thermus thermophilus HB8 | Descriptor: | Alpha-ribazole-5'-phosphate phosphatase, GLYCEROL, SODIUM ION | Authors: | Sugahara, M, Taketa, M, Tanaka, Y, Matsuura, Y, Kunishima, N, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2007-03-08 | Release date: | 2007-09-11 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.75 Å) | Cite: | Crystal structure of TTHB049 from Thermus thermophilus HB8 To be Published
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3GP7
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4G5H
| Crystal structure of capsular polysaccharide synthesizing enzyme CapE from Staphylococcus aureus in complex with by-product | Descriptor: | Capsular polysaccharide synthesis enzyme Cap8E, FORMIC ACID, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, ... | Authors: | Miyafusa, T, Caaveiro, J.M.M, Tanaka, Y, Tsumoto, K. | Deposit date: | 2012-07-18 | Release date: | 2013-08-28 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (1.88 Å) | Cite: | Dynamic elements govern the catalytic activity of CapE, a capsular polysaccharide-synthesizing enzyme from Staphylococcus aureus. Febs Lett., 587, 2013
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6AIT
| Crystal structure of E. coli BepA | Descriptor: | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, Beta-barrel assembly-enhancing protease, ZINC ION | Authors: | Umar, M.S.M, Tanaka, Y, Kamikubo, H, Tsukazaki, T. | Deposit date: | 2018-08-24 | Release date: | 2018-12-26 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.598 Å) | Cite: | Structural Basis for the Function of the beta-Barrel Assembly-Enhancing Protease BepA. J. Mol. Biol., 431, 2019
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7WAG
| Crystal structure of MurJ squeezed form | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, DI(HYDROXYETHYL)ETHER, Lipid II flippase MurJ | Authors: | Tsukazaki, T, Kohga, H, Tanaka, Y, Yoshikaie, K, Taniguchi, K, Fujimoto, K. | Deposit date: | 2021-12-14 | Release date: | 2022-06-01 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.55 Å) | Cite: | Crystal structure of the lipid flippase MurJ in a "squeezed" form distinct from its inward- and outward-facing forms. Structure, 30, 2022
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7WAW
| MurJ inward closed form | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, lipid II flippase MurJ | Authors: | Tsukazaki, T, Kohga, H, Tanaka, Y, Yoshikaie, K, Taniguchi, K, Fujimoto, K. | Deposit date: | 2021-12-15 | Release date: | 2022-06-01 | Last modified: | 2022-08-17 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Crystal structure of the lipid flippase MurJ in a "squeezed" form distinct from its inward- and outward-facing forms. Structure, 30, 2022
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7WAX
| MurJ inward occluded form | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, (4S)-2-METHYL-2,4-PENTANEDIOL, lipid II flippase MurJ | Authors: | Tsukazaki, T, Kohga, H, Tanaka, Y, Yoshikaie, K, Taniguchi, K, Fujimoto, K. | Deposit date: | 2021-12-15 | Release date: | 2022-06-01 | Last modified: | 2022-08-17 | Method: | X-RAY DIFFRACTION (2.35 Å) | Cite: | Crystal structure of the lipid flippase MurJ in a "squeezed" form distinct from its inward- and outward-facing forms. Structure, 30, 2022
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3BIS
| Crystal Structure of the PD-L1 | Descriptor: | Programmed cell death 1 ligand 1 | Authors: | Lin, D.Y, Tanaka, Y, Iwasaki, M, Gittis, A.G, Su, H.P, Mikami, B, Okazaki, T, Honjo, T, Minato, N, Garboczi, D.N. | Deposit date: | 2007-11-30 | Release date: | 2008-02-26 | Last modified: | 2011-07-13 | Method: | X-RAY DIFFRACTION (2.64 Å) | Cite: | The PD-1/PD-L1 complex resembles the antigen-binding Fv domains of antibodies and T cell receptors. Proc.Natl.Acad.Sci.Usa, 105, 2008
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4L24
| Crystal structure of metallo-DNA duplex containing consecutive T-Hg(II)-T base pairs | Descriptor: | DNA (5'-D(*CP*GP*CP*GP*AP*TP*TP*TP*CP*GP*CP*G)-3'), MERCURY (II) ION | Authors: | Kondo, J, Yamada, T, Hirose, C, Okamoto, I, Tanaka, Y, Ono, A. | Deposit date: | 2013-06-04 | Release date: | 2014-03-05 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.7 Å) | Cite: | Crystal Structure of Metallo DNA Duplex Containing Consecutive Watson-Crick-like T-Hg(II) -T Base Pairs Angew.Chem.Int.Ed.Engl., 53, 2014
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4L26
| Crystal structure of DNA duplex containing consecutive T-T mispairs (Br-derivative) | Descriptor: | DNA (5'-D(*CP*GP*(CBR)P*GP*AP*TP*TP*TP*CP*GP*CP*G)-3') | Authors: | Kondo, J, Yamada, T, Hirose, C, Tanaka, Y, Ono, A. | Deposit date: | 2013-06-04 | Release date: | 2014-03-05 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (1.4 Å) | Cite: | Crystal Structure of Metallo DNA Duplex Containing Consecutive Watson-Crick-like T-Hg(II) -T Base Pairs Angew.Chem.Int.Ed.Engl., 53, 2014
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4L25
| Crystal structure of DNA duplex containing consecutive T-T mispairs | Descriptor: | DNA (5'-D(*CP*GP*CP*GP*AP*TP*TP*TP*CP*GP*CP*G)-3') | Authors: | Kondo, J, Yamada, T, Hirose, C, Tanaka, Y, Ono, A. | Deposit date: | 2013-06-04 | Release date: | 2014-03-05 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.1 Å) | Cite: | Crystal Structure of Metallo DNA Duplex Containing Consecutive Watson-Crick-like T-Hg(II) -T Base Pairs Angew.Chem.Int.Ed.Engl., 53, 2014
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2RT8
| Structure of metallo-dna in solution | Descriptor: | DNA (5'-D(*CP*GP*CP*GP*TP*TP*GP*TP*CP*C)-3'), DNA (5'-D(*GP*GP*AP*CP*TP*TP*CP*GP*CP*G)-3'), MERCURY (II) ION | Authors: | Yamaguchi, H, Sebera, J, Kondo, J, Oda, S, Komuro, T, Kawamura, T, Dairaku, T, Kondo, Y, Okamoto, I, Ono, A, Burda, J.V, Kojima, C, Sychrovsky, V, Tanaka, Y. | Deposit date: | 2013-06-18 | Release date: | 2014-03-05 | Last modified: | 2023-06-14 | Method: | SOLUTION NMR | Cite: | The structure of metallo-DNA with consecutive thymine-HgII-thymine base pairs explains positive entropy for the metallo base pair formation. Nucleic Acids Res., 42, 2014
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2RVP
| Solution structure of DNA Containing Metallo-Base-Pair | Descriptor: | DNA (5'-D(*TP*AP*AP*TP*AP*TP*AP*CP*TP*TP*AP*AP*TP*TP*A)-3'), DNA (5'-D(*TP*AP*AP*TP*TP*AP*AP*CP*TP*AP*TP*AP*TP*TP*A)-3'), SILVER ION | Authors: | Dairaku, T, Furuita, K, Sato, H, Sebera, J, Nakashima, K, Kondo, J, Yamanaka, D, Kondo, Y, Okamoto, I, Ono, A, Sychrovsky, V, Kojima, C, Tanaka, Y. | Deposit date: | 2016-03-22 | Release date: | 2016-08-31 | Last modified: | 2023-06-14 | Method: | SOLUTION NMR | Cite: | Structure Determination of an Ag(I) -Mediated Cytosine-Cytosine Base Pair within DNA Duplex in Solution with (1) H/(15) N/(109) Ag NMR Spectroscopy. Chemistry, 22, 2016
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6IDS
| Crystal structure of Vibrio cholerae MATE transporter VcmN D35N mutant | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, MATE family efflux transporter | Authors: | Kusakizako, T, Claxton, D.P, Tanaka, Y, Maturana, A.D, Kuroda, T, Ishitani, R, Mchaourab, H.S, Nureki, O. | Deposit date: | 2018-09-11 | Release date: | 2019-01-16 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (2.79 Å) | Cite: | Structural Basis of H+-Dependent Conformational Change in a Bacterial MATE Transporter. Structure, 27, 2019
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