5VUC
| Pim1 Kinase in complex with a benzofuranone inhibitor | Descriptor: | (2Z)-2-(1H-indol-3-ylmethylidene)-6-methoxy-7-(piperazin-1-ylmethyl)-1-benzofuran-3-one, GLYCEROL, Serine/threonine-protein kinase pim-1 | Authors: | Parker, L.J. | Deposit date: | 2017-05-18 | Release date: | 2017-12-13 | Last modified: | 2018-01-17 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Theoretical Analysis of Activity Cliffs among Benzofuranone-Class Pim1 Inhibitors Using the Fragment Molecular Orbital Method with Molecular Mechanics Poisson-Boltzmann Surface Area (FMO+MM-PBSA) Approach J Chem Inf Model, 57, 2017
|
|
1UJ4
| Crystal structure of Thermus thermophilus ribose-5-phosphate isomerase | Descriptor: | CHLORIDE ION, ribose 5-phosphate isomerase | Authors: | Hamada, K, Ago, H, Sugahara, M, Nodake, Y, Kuramitsu, S, Yokoyama, S, Miyano, M, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2003-07-26 | Release date: | 2004-07-13 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Oxyanion hole-stabilized stereospecific isomerization in ribose-5-phosphate isomerase (Rpi) J.Biol.Chem., 278, 2003
|
|
1UJ6
| Crystal structure of Thermus thermophilus ribose-5-phosphate isomerase complexed with arabinose-5-phosphate | Descriptor: | ARABINOSE-5-PHOSPHATE, CHLORIDE ION, ribose 5-phosphate isomerase | Authors: | Hamada, K, Ago, H, Sugahara, M, Nodake, Y, Kuramitsu, S, Yokoyama, S, Miyano, M, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2003-07-26 | Release date: | 2004-07-13 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (1.74 Å) | Cite: | Oxyanion hole-stabilized stereospecific isomerization in ribose-5-phosphate isomerase (Rpi) J.Biol.Chem., 278, 2003
|
|
1UJ5
| Crystal structure of Thermus thermophilus ribose-5-phosphate isomerase complexed with ribose-5-phosphate | Descriptor: | CHLORIDE ION, RIBULOSE-5-PHOSPHATE, ribose 5-phosphate isomerase | Authors: | Hamada, K, Ago, H, Sugahara, M, Nodake, Y, Kuramitsu, S, Yokoyama, S, Miyano, M, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2003-07-26 | Release date: | 2004-07-13 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Oxyanion hole-stabilized stereospecific isomerization in ribose-5-phosphate isomerase (Rpi) J.Biol.Chem., 278, 2003
|
|
1UJP
| Crystal Structure of Tryptophan Synthase A-Subunit From Thermus thermophilus HB8 | Descriptor: | CITRIC ACID, Tryptophan synthase alpha chain | Authors: | Asada, Y, Yokoyama, S, Kuramitsu, S, Miyano, M, Kunishima, N, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2003-08-08 | Release date: | 2003-08-26 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.34 Å) | Cite: | Stabilization mechanism of the tryptophan synthase alpha-subunit from Thermus thermophilus HB8: X-ray crystallographic analysis and calorimetry. J.Biochem.(Tokyo), 138, 2005
|
|
6KGR
| LSD1-FCPA-MPE N5 adduct model | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, 3-[4-[5-fluoranyl-2-(trifluoromethyl)phenyl]phenyl]propanal, FLAVIN-ADENINE DINUCLEOTIDE, ... | Authors: | Niwa, H, Sato, S, Handa, N, Umehara, T. | Deposit date: | 2019-07-12 | Release date: | 2020-03-25 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (2.32 Å) | Cite: | Development and Structural Evaluation of N-Alkylated trans-2-Phenylcyclopropylamine-Based LSD1 Inhibitors. Chemmedchem, 15, 2020
|
|
6KGP
| LSD1-S2157 N5 adduct model | Descriptor: | 3-[3,5-bis(fluoranyl)-2-phenylmethoxy-phenyl]propanal, FLAVIN-ADENINE DINUCLEOTIDE, GLYCEROL, ... | Authors: | Niwa, H, Sato, S, Umehara, T. | Deposit date: | 2019-07-12 | Release date: | 2020-03-25 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (2.25 Å) | Cite: | Development and Structural Evaluation of N-Alkylated trans-2-Phenylcyclopropylamine-Based LSD1 Inhibitors. Chemmedchem, 15, 2020
|
|
6KGO
| LSD1-S2157 five-membered ring adduct model | Descriptor: | 3-[3,5-bis(fluoranyl)-2-phenylmethoxy-phenyl]propanal, FLAVIN-ADENINE DINUCLEOTIDE, GLYCEROL, ... | Authors: | Niwa, H, Sato, S, Umehara, T. | Deposit date: | 2019-07-12 | Release date: | 2020-03-25 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (2.25 Å) | Cite: | Development and Structural Evaluation of N-Alkylated trans-2-Phenylcyclopropylamine-Based LSD1 Inhibitors. Chemmedchem, 15, 2020
|
|
5AVM
| Crystal structures of 5-aminoimidazole ribonucleotide (AIR) synthetase, PurM, from Thermus thermophilus | Descriptor: | Phosphoribosylformylglycinamidine cyclo-ligase, SULFATE ION | Authors: | Kanagawa, M, Baba, S, Watanabe, Y, Nakagawa, N, Ebihara, A, Sampei, G, Kawai, G, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2015-06-23 | Release date: | 2015-11-25 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Crystal structures and ligand binding of PurM proteins from Thermus thermophilus and Geobacillus kaustophilus J.Biochem., 159, 2016
|
|
6KGN
| LSD1-CoREST-S2116 N5 adduct model | Descriptor: | 3-[3,5-bis(fluoranyl)-2-phenylmethoxy-phenyl]propanal, FLAVIN-ADENINE DINUCLEOTIDE, GLYCEROL, ... | Authors: | Niwa, H, Sato, S, Umehara, T. | Deposit date: | 2019-07-12 | Release date: | 2020-03-25 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (2.62 Å) | Cite: | Development and Structural Evaluation of N-Alkylated trans-2-Phenylcyclopropylamine-Based LSD1 Inhibitors. Chemmedchem, 15, 2020
|
|
6KGQ
| LSD1-FCPA-MPE five-membered ring adduct model | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, 3-[4-[5-fluoranyl-2-(trifluoromethyl)phenyl]phenyl]propanal, FLAVIN-ADENINE DINUCLEOTIDE, ... | Authors: | Niwa, H, Sato, S, Handa, N, Umehara, T. | Deposit date: | 2019-07-12 | Release date: | 2020-03-25 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (2.32 Å) | Cite: | Development and Structural Evaluation of N-Alkylated trans-2-Phenylcyclopropylamine-Based LSD1 Inhibitors. Chemmedchem, 15, 2020
|
|
3EOQ
| The crystal structure of putative zinc protease beta-subunit from Thermus thermophilus HB8 | Descriptor: | Putative zinc protease | Authors: | Ohtsuka, J, Ichihara, Y, Ebihara, A, Yokoyama, S, Kuramitsu, S, Nagata, K, Tanokura, M. | Deposit date: | 2008-09-29 | Release date: | 2009-03-17 | Last modified: | 2011-07-13 | Method: | X-RAY DIFFRACTION (2.29 Å) | Cite: | Crystal structure of TTHA1264, a putative M16-family zinc peptidase from Thermus thermophilus HB8 that is homologous to the beta subunit of mitochondrial processing peptidase. Proteins, 2009
|
|
6KGM
| LSD1-CoREST-S2116 five-membered ring adduct model | Descriptor: | 3-[3,5-bis(fluoranyl)-2-phenylmethoxy-phenyl]propanal, FLAVIN-ADENINE DINUCLEOTIDE, GLYCEROL, ... | Authors: | Niwa, H, Sato, S, Umehara, T. | Deposit date: | 2019-07-12 | Release date: | 2020-03-25 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (2.62 Å) | Cite: | Development and Structural Evaluation of N-Alkylated trans-2-Phenylcyclopropylamine-Based LSD1 Inhibitors. Chemmedchem, 15, 2020
|
|
1UJN
| Crystal structure of dehydroquinate synthase from Thermus thermophilus HB8 | Descriptor: | dehydroquinate synthase | Authors: | Sugahara, M, Yokoyama, S, Kuramitsu, S, Miyano, M, Kunishima, N, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2003-08-06 | Release date: | 2003-09-02 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Crystal structure of dehydroquinate synthase from Thermus thermophilus HB8 showing functional importance of the dimeric state. Proteins, 58, 2005
|
|
1UKK
| Structure of Osmotically Inducible Protein C from Thermus thermophilus | Descriptor: | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, Osmotically Inducible Protein C | Authors: | Rehse, P.H, Kuramitsu, S, Yokoyama, S, Miyano, M, Tahirov, T.H, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | Deposit date: | 2003-08-24 | Release date: | 2004-05-04 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (1.6 Å) | Cite: | Crystallographic Structure and Biochemical Analysis of the Thermus thermophilus Osmotically Inducible Protein C J.MOL.BIOL., 338, 2004
|
|
2HHH
| Crystal structure of kasugamycin bound to the 30S ribosomal subunit | Descriptor: | (1S,2R,3S,4R,5S,6S)-2,3,4,5,6-PENTAHYDROXYCYCLOHEXYL 2-AMINO-4-{[CARBOXY(IMINO)METHYL]AMINO}-2,3,4,6-TETRADEOXY-ALPHA-D-ARABINO-HEXOPYRANOSIDE, 16S ribosomal RNA, 30S ribosomal protein S10, ... | Authors: | Schluenzen, F. | Deposit date: | 2006-06-28 | Release date: | 2006-09-26 | Last modified: | 2024-04-03 | Method: | X-RAY DIFFRACTION (3.35 Å) | Cite: | The antibiotic kasugamycin mimics mRNA nucleotides to destabilize tRNA binding and inhibit canonical translation initiation. Nat.Struct.Mol.Biol., 13, 2006
|
|
5XDN
| Crystal structure of human voltage-dependent anion channel 1 (hVDAC1) in P22121 space group | Descriptor: | DECANE, DODECANE, HEXANE, ... | Authors: | Hosaka, T, Kimura-Someya, T, Shirouzu, M. | Deposit date: | 2017-03-28 | Release date: | 2017-06-28 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (3.15 Å) | Cite: | Crystal structural characterization reveals novel oligomeric interactions of human voltage-dependent anion channel 1 Protein Sci., 26, 2017
|
|
5AYQ
| |
5XDO
| Crystal structure of human voltage-dependent anion channel 1 (hVDAC1) in C222 space group | Descriptor: | HEXANE, N-OCTANE, PENTANE, ... | Authors: | Hosaka, T, Kimura-Someya, T, Shirouzu, M. | Deposit date: | 2017-03-28 | Release date: | 2017-06-28 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (3.1 Å) | Cite: | Crystal structural characterization reveals novel oligomeric interactions of human voltage-dependent anion channel 1 Protein Sci., 26, 2017
|
|
1IW7
| |
4NZY
| Crystal structure (type-2) of dTMP kinase (st1543) from Sulfolobus Tokodaii Strain7 | Descriptor: | 1,2-ETHANEDIOL, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, DI(HYDROXYETHYL)ETHER, ... | Authors: | Biswas, A, Jeyakanthan, J, Sekar, K, Kuramitsu, S, Yokoyama, S. | Deposit date: | 2013-12-13 | Release date: | 2014-12-24 | Last modified: | 2024-02-28 | Method: | X-RAY DIFFRACTION (2.15 Å) | Cite: | Insight into Substrate Binding Mechanism in Thymidylate Kinase based on Intrinsic Dynamics of the Active Site To be Published
|
|
5B2N
| Crystal structure of the light-driven chloride ion-pumping rhodopsin, ClP, from Nonlabens marinus | Descriptor: | CHLORIDE ION, Chloride pumping rhodopsin, DECANE, ... | Authors: | Hosaka, T, Kimura-Someya, T, Shirouzu, M. | Deposit date: | 2016-01-20 | Release date: | 2016-07-13 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.581 Å) | Cite: | Structural Mechanism for Light-driven Transport by a New Type of Chloride Ion Pump, Nonlabens marinus Rhodopsin-3 J.Biol.Chem., 291, 2016
|
|
1UB7
| |
2OM7
| Structural Basis for Interaction of the Ribosome with the Switch Regions of GTP-bound Elongation Factors | Descriptor: | 16S ribosomal RNA (H5), 30S ribosomal protein S12, 30S ribosomal protein S2, ... | Authors: | Connell, S.R, Wilson, D.N, Rost, M, Schueler, M, Giesebrecht, J, Dabrowski, M, Mielke, T, Fucini, P, Spahn, C.M.T. | Deposit date: | 2007-01-21 | Release date: | 2008-01-15 | Last modified: | 2023-12-27 | Method: | ELECTRON MICROSCOPY (7.3 Å) | Cite: | Structural basis for interaction of the ribosome with the switch regions of GTP-bound elongation factors. Mol.Cell, 25, 2007
|
|
5YE4
| Crystal structure of the complex of di-acetylated histone H4 and 1A9D7 Fab fragment | Descriptor: | 1A9D7 L chain, 1A9D7 VH CH1 chain, ZINC ION, ... | Authors: | Matsuda, T, Ito, T, Wakamori, M, Umehara, T. | Deposit date: | 2017-09-15 | Release date: | 2018-08-22 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.799 Å) | Cite: | JQ1 affects BRD2-dependent and independent transcription regulation without disrupting H4-hyperacetylated chromatin states. Epigenetics, 13, 2018
|
|