2PCN
 
 | | Crystal structure of S-adenosylmethionine: 2-dimethylmenaquinone methyltransferase (gk_1813) from geobacillus kaustophilus HTA426 | | Descriptor: | ACETATE ION, S-adenosylmethionine:2-demethylmenaquinone methyltransferase | | Authors: | Jeyakanthan, J, Kanaujia, S.P, Rafi, Z.A, Sekar, K, Agari, Y, Ebihara, A, Kuramitsu, S, Shinkai, A, Shiro, Y, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2007-03-30 | | Release date: | 2007-10-02 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Crystal structure of S-adenosylmethionine:2-dimethylmenaquinone methyltransferase (gk_1813) from geobacillus kaustophilus HTA426
To be Published
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6AJV
 | | Crystal structure of BRD4 in complex with isoliquiritigenin and DMSO (Cocktail No. 3) | | Descriptor: | 2',4,4'-TRIHYDROXYCHALCONE, Bromodomain-containing protein 4, DIMETHYL SULFOXIDE, ... | | Authors: | Yokoyama, T, Matsumoto, K, Nabeshima, Y, Mizuguchi, M. | | Deposit date: | 2018-08-28 | | Release date: | 2019-06-12 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (1.45 Å) | | Cite: | Structural and thermodynamic characterization of the binding of isoliquiritigenin to the first bromodomain of BRD4.
Febs J., 286, 2019
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6AJX
 | | Crystal structure of BRD4 in complex with isoliquiritigenin in the absence of DMSO | | Descriptor: | 2',4,4'-TRIHYDROXYCHALCONE, Bromodomain-containing protein 4, SODIUM ION | | Authors: | Yokoyama, T, Matsumoto, K, Nabeshima, Y, Mizuguchi, M. | | Deposit date: | 2018-08-28 | | Release date: | 2019-06-12 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (1.887 Å) | | Cite: | Structural and thermodynamic characterization of the binding of isoliquiritigenin to the first bromodomain of BRD4.
Febs J., 286, 2019
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6AJY
 | | Crystal structure of BRD4 in complex with 2',4'-dihydroxy-2-methoxychalcone | | Descriptor: | 2',4'-dihydroxy-2-methoxychalcone, Bromodomain-containing protein 4, SODIUM ION | | Authors: | Yokoyama, T, Matsumoto, K, Nabeshima, Y, Mizuguchi, M. | | Deposit date: | 2018-08-28 | | Release date: | 2019-06-12 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Structural and thermodynamic characterization of the binding of isoliquiritigenin to the first bromodomain of BRD4.
Febs J., 286, 2019
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6AJZ
 | | Joint nentron and X-ray structure of BRD4 in complex with colchicin | | Descriptor: | Bromodomain-containing protein 4, N-[(7S)-1,2,3,10-tetramethoxy-9-oxo-6,7-dihydro-5H-benzo[d]heptalen-7-yl]ethanamide, SODIUM ION | | Authors: | Yokoyama, T, Ostermann, A, Schrader, T.E, Nabeshima, Y, Mizuguchi, M. | | Deposit date: | 2018-08-28 | | Release date: | 2019-06-12 | | Last modified: | 2024-03-27 | | Method: | NEUTRON DIFFRACTION (1.301 Å), X-RAY DIFFRACTION | | Cite: | Structural and thermodynamic characterization of the binding of isoliquiritigenin to the first bromodomain of BRD4.
Febs J., 286, 2019
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3VHM
 | | Crystal structure of NPC-biotin-avidin complex | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 5-[(3aS,4R,6aR)-1-{[(1R)-1-(6-nitro-1,3-benzodioxol-5-yl)ethoxy]carbonyl}-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid, Avidin, ... | | Authors: | Terai, T, Maki, E, Sugiyama, S, Takahashi, Y, Matsumura, H, Mori, Y, Nagano, T. | | Deposit date: | 2011-08-29 | | Release date: | 2011-12-28 | | Last modified: | 2020-07-29 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Rational development of caged-biotin protein-labeling agents and some applications in live cells
Chem.Biol., 18, 2011
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6AJW
 | | Crystal structure of BRD4 in complex with DMSO (Cocktail No. 4) | | Descriptor: | Bromodomain-containing protein 4, DIMETHYL SULFOXIDE, SODIUM ION | | Authors: | Yokoyama, T, Matsumoto, K, Nabeshima, Y, Mizuguchi, M. | | Deposit date: | 2018-08-28 | | Release date: | 2019-06-12 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (1.401 Å) | | Cite: | Structural and thermodynamic characterization of the binding of isoliquiritigenin to the first bromodomain of BRD4.
Febs J., 286, 2019
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7E5O
 | | Crystal structure of SARS-CoV-2 RBD in complex with antibody NT-193 | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, NT-193 Heavy chain, NT-193 Light chain, ... | | Authors: | Kita, S, Onodera, T, Adachi, Y, Moriayma, S, Nomura, T, Tadokoro, T, Anraku, Y, Yumoto, K, Tian, C, Fukuhara, H, Suzuki, T, Tonouchi, K, Sasaki, J, Sun, L, Hashiguchi, T, Takahashi, Y, Maenaka, K. | | Deposit date: | 2021-02-19 | | Release date: | 2021-09-08 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | A SARS-CoV-2 antibody broadly neutralizes SARS-related coronaviruses and variants by coordinated recognition of a virus-vulnerable site.
Immunity, 54, 2021
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2MLQ
 | | Human CCR2 Membrane-Proximal C-Terminal Region (PRO-C) in a frount bound form | | Descriptor: | MCP-1 receptor | | Authors: | Esaki, K, Yoshinaga, S, Tsuji, T, Toda, E, Terashima, Y, Saitoh, T, Kohda, D, Kohno, T, Osawa, M, Ueda, T, Shimada, I, Matsushima, K, Terasawa, H. | | Deposit date: | 2014-03-04 | | Release date: | 2014-10-08 | | Last modified: | 2024-05-15 | | Method: | SOLUTION NMR | | Cite: | Structural basis for the binding of the membrane-proximal C-terminal region of chemokine receptor CCR2 with the cytosolic regulator FROUNT.
Febs J., 281, 2014
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2MLO
 | | Human CCR2 Membrane-Proximal C-Terminal Region (PRO-C) in a Membrane bound form | | Descriptor: | MCP-1 receptor | | Authors: | Esaki, K, Yoshinaga, S, Tsuji, T, Toda, E, Terashima, Y, Saitoh, T, Kohda, D, Kohno, T, Osawa, M, Ueda, T, Shimada, I, Matsushima, K, Terasawa, H. | | Deposit date: | 2014-03-04 | | Release date: | 2014-10-08 | | Last modified: | 2024-05-15 | | Method: | SOLUTION NMR | | Cite: | Structural basis for the binding of the membrane-proximal C-terminal region of chemokine receptor CCR2 with the cytosolic regulator FROUNT.
Febs J., 281, 2014
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3WSP
 | | Crystal Structure of P450BM3 with N-perfluorononanoyl-L-tryptophan | | Descriptor: | Bifunctional P-450/NADPH-P450 reductase, DIMETHYL SULFOXIDE, N-(2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,9-heptadecafluorononanoyl)-L-tryptophan, ... | | Authors: | Cong, Z, Shoji, O, Kasai, C, Sugimoto, H, Shiro, Y, Watanabe, Y. | | Deposit date: | 2014-03-20 | | Release date: | 2014-11-26 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Activation of Wild-type Cytochrome P450BM3 by the Next Generation of Decoy Molecules: Enhanced Hydroxylation of Gaseous Alkanes and Crystallographic Evidence.
ACS CATALYSIS, 5, 2015
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7BYY
 | | Crystal structure of bacterial toxin | | Descriptor: | Acetyltransferase | | Authors: | Zhang, C, Yashiro, Y, Tomita, K. | | Deposit date: | 2020-04-25 | | Release date: | 2020-06-03 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.799 Å) | | Cite: | Substrate specificities of Escherichia coli ItaT that acetylates aminoacyl-tRNAs.
Nucleic Acids Res., 48, 2020
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6BN3
 | | CTX-M-151 class A extended-spectrum beta-lactamase apo crystal structure at 1.3 Angstrom resolution | | Descriptor: | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, Beta-lactamase | | Authors: | Power, P, Ghiglione, B, Rodriguez, M.M, Gutkind, G, Ishii, Y, Bonomo, R.A, Klinke, S. | | Deposit date: | 2017-11-16 | | Release date: | 2018-11-21 | | Last modified: | 2024-05-22 | | Method: | X-RAY DIFFRACTION (1.278 Å) | | Cite: | Structural and Biochemical Characterization of the Novel CTX-M-151 Extended-Spectrum beta-Lactamase and Its Inhibition by Avibactam.
Antimicrob.Agents Chemother., 65, 2021
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3WP9
 | | Crystal structure of antifreeze protein from an Antarctic sea ice bacterium Colwellia sp. | | Descriptor: | Ice-binding protein | | Authors: | Hanada, Y, Nishimiya, Y, Miura, A, Tsuda, S, Kondo, H. | | Deposit date: | 2014-01-10 | | Release date: | 2014-07-02 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Hyperactive antifreeze protein from an Antarctic sea ice bacterium Colwellia sp. has a compound ice-binding site without repetitive sequences.
Febs J., 281, 2014
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6BPF
 | | CTX-M-151 class A extended-spectrum beta-lactamase crystal structure in complex with avibactam at 1.32 Angstrom resolution | | Descriptor: | (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide, Beta-lactamase | | Authors: | Power, P, Ghiglione, B, Rodriguez, M.M, Gutkind, G, Ishii, Y, Bonomo, R.A, Klinke, S. | | Deposit date: | 2017-11-23 | | Release date: | 2018-11-28 | | Last modified: | 2023-10-04 | | Method: | X-RAY DIFFRACTION (1.318 Å) | | Cite: | Structural and Biochemical Characterization of the Novel CTX-M-151 Extended-Spectrum beta-Lactamase and Its Inhibition by Avibactam.
Antimicrob.Agents Chemother., 65, 2021
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1D06
 | | STRUCTURAL BASIS OF DIMERIZATION AND SENSORY MECHANISMS OF OXYGEN-SENSING DOMAIN OF RHIZOBIUM MELILOTI FIXL DETERMINED AT 1.4A RESOLUTION | | Descriptor: | PROTOPORPHYRIN IX CONTAINING FE, nitrogen fixation regulatory protein fixL | | Authors: | Miyatake, H, Mukai, M, Park, S.-Y, Adachi, S, Tamura, K, Nakamura, H, Nakamura, K, Tsuchiya, T, Iizuka, T, Shiro, Y. | | Deposit date: | 1999-09-09 | | Release date: | 2000-03-15 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (1.4 Å) | | Cite: | Sensory mechanism of oxygen sensor FixL from Rhizobium meliloti: crystallographic, mutagenesis and resonance Raman spectroscopic studies
J.MOL.BIOL., 301, 2000
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2FEI
 | | Solution structure of the second SH3 domain of Human CMS protein | | Descriptor: | CD2-associated protein | | Authors: | Yao, B, Dai, H, Jiao, Y, Wu, J, Shi, Y. | | Deposit date: | 2005-12-15 | | Release date: | 2006-12-05 | | Last modified: | 2024-05-29 | | Method: | SOLUTION NMR | | Cite: | Solution structure of the second SH3 domain of human CMS and a newly identified binding site at the C-terminus of c-Cbl
Biochim.Biophys.Acta, 1774, 2007
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1DQ3
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3VOR
 | | Crystal Structure Analysis of the CofA | | Descriptor: | CFA/III pilin | | Authors: | Fukakusa, S, Kawahara, K, Nakamura, S, Iwasita, T, Baba, S, Nishimura, M, Kobayashi, Y, Honda, T, Iida, T, Taniguchi, T, Ohkubo, T. | | Deposit date: | 2012-02-06 | | Release date: | 2012-09-26 | | Last modified: | 2013-07-31 | | Method: | X-RAY DIFFRACTION (0.9 Å) | | Cite: | Structure of the CFA/III major pilin subunit CofA from human enterotoxigenic Escherichia coli determined at 0.90 A resolution by sulfur-SAD phasing
Acta Crystallogr.,Sect.D, 68, 2012
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7DVU
 | | Crystal structure of heme sensor protein PefR in complex with heme and cyanide | | Descriptor: | CYANIDE ION, HTH marR-type domain-containing protein, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Nishinaga, M, Nagai, S, Nishitani, Y, Sugimoto, H, Shiro, Y, Sawai, H. | | Deposit date: | 2021-01-15 | | Release date: | 2021-09-29 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Heme controls the structural rearrangement of its sensor protein mediating the hemolytic bacterial survival.
Commun Biol, 4, 2021
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7DVT
 | | Crystal structure of heme sensor protein PefR in complex with heme and carbon monoxide | | Descriptor: | CARBON MONOXIDE, HTH marR-type domain-containing protein, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Nishinaga, M, Nagai, S, Nishitani, Y, Sugimoto, H, Shiro, Y, Sawai, H. | | Deposit date: | 2021-01-15 | | Release date: | 2021-09-29 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.09 Å) | | Cite: | Heme controls the structural rearrangement of its sensor protein mediating the hemolytic bacterial survival.
Commun Biol, 4, 2021
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7DVR
 | | Crystal structure of heme sensor protein PefR from Streptococcus agalactiae in complex with heme | | Descriptor: | COBALT (II) ION, HTH marR-type domain-containing protein, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Nishinaga, M, Nagai, S, Nishitani, Y, Sugimoto, H, Shiro, Y, Sawai, H. | | Deposit date: | 2021-01-15 | | Release date: | 2021-09-29 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Heme controls the structural rearrangement of its sensor protein mediating the hemolytic bacterial survival.
Commun Biol, 4, 2021
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7DVV
 | | Heme sensor protein PefR from Streptococcus agalactiae bound to operator DNA (28-mer) | | Descriptor: | DNA (28-MER), HTH marR-type domain-containing protein | | Authors: | Nishinaga, M, Nagai, S, Nishitani, Y, Sugimoto, H, Shiro, Y, Sawai, H. | | Deposit date: | 2021-01-15 | | Release date: | 2021-09-29 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.49 Å) | | Cite: | Heme controls the structural rearrangement of its sensor protein mediating the hemolytic bacterial survival.
Commun Biol, 4, 2021
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3W6V
 | | Crystal structure of the DNA-binding domain of AdpA, the global transcriptional factor, in complex with a target DNA | | Descriptor: | AdpA, DNA (5'-D(*AP*GP*GP*TP*TP*GP*GP*CP*GP*GP*GP*TP*TP*CP*AP*C)-3'), DNA (5'-D(*CP*TP*GP*TP*GP*AP*AP*CP*CP*CP*GP*CP*CP*AP*AP*C)-3') | | Authors: | Yao, M.D, Ohtsuka, J, Nagata, K, Miyazono, K, Ohnishi, Y, Tanokura, M. | | Deposit date: | 2013-02-22 | | Release date: | 2013-09-18 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.95 Å) | | Cite: | Complex Structure of the DNA-binding Domain of AdpA, the Global Transcription Factor in Streptomyces griseus, and a Target Duplex DNA Reveals the Structural Basis of Its Tolerant DNA Sequence Specificity
J.Biol.Chem., 288, 2013
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1IZO
 | | Cytochrome P450 BS beta Complexed with Fatty Acid | | Descriptor: | Cytochrome P450 152A1, PALMITOLEIC ACID, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Lee, D.S, Yamada, A, Sugimoto, H, Matsunaga, I, Ogura, H, Ichihara, K, Adachi, S, Park, S.Y, Shiro, Y, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2002-10-10 | | Release date: | 2003-03-18 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Substrate Recognition and Molecular Mechanism of Fatty Acid Hydroxylation by Cytochrome P450 from Bacillus subtilis. CRYSTALLOGRAPHIC, SPECTROSCOPIC, AND MUTATIONAL STUDIES.
J.Biol.Chem., 278, 2003
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