6M2P
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 6m2p by Molmil](/molmil-images/mine/6m2p) | Crystal structure of a NIR-emitting DNA-stabilized Ag16 nanocluster (A10-deletion mutant) | Descriptor: | CALCIUM ION, CHLORIDE ION, DNA (5'-D(*CP*AP*CP*CP*TP*AP*GP*CP*G)-3'), ... | Authors: | Kondo, J, Cerretani, C, Vosch, T. | Deposit date: | 2020-02-28 | Release date: | 2020-07-01 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.13 Å) | Cite: | Removal of the A10 adenosine in a DNA-stabilized Ag16 nanocluster. Rsc Adv, 10, 2020
|
|
2G5K
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 2g5k by Molmil](/molmil-images/mine/2g5k) | Crystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site complexed with Apramycin | Descriptor: | 5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3', APRAMYCIN, COBALT HEXAMMINE(III), ... | Authors: | Kondo, J, Francois, B, Urzhumtsev, A, Westhof, E. | Deposit date: | 2006-02-23 | Release date: | 2006-06-20 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Crystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site Complexed with Apramycin Angew.Chem.Int.Ed.Engl., 45, 2006
|
|
4GPW
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 4gpw by Molmil](/molmil-images/mine/4gpw) | Crystal structure of the protozoal cytoplasmic ribosomal decoding site in complex with 6'-hydroxysisomicin (P21212 form) | Descriptor: | (1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(hydroxymethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside, RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3') | Authors: | Kondo, J, Koganei, M, Maianti, J.P, Ly, V.L, Hanessian, S. | Deposit date: | 2012-08-22 | Release date: | 2013-04-03 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (3 Å) | Cite: | Crystal structures of a bioactive 6'-hydroxy variant of sisomicin bound to the bacterial and protozoal ribosomal decoding sites Chemmedchem, 8, 2013
|
|
4GPY
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 4gpy by Molmil](/molmil-images/mine/4gpy) | Crystal structure of the bacterial ribosomal decoding site in complex with 6'-hydroxysisomicin | Descriptor: | (1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(hydroxymethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside, RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3') | Authors: | Kondo, J, Koganei, M, Maianti, J.P, Ly, V.L, Hanessian, S. | Deposit date: | 2012-08-22 | Release date: | 2013-04-03 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Crystal structures of a bioactive 6'-hydroxy variant of sisomicin bound to the bacterial and protozoal ribosomal decoding sites Chemmedchem, 8, 2013
|
|
2GOT
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 2got by Molmil](/molmil-images/mine/2got) | |
4P3U
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 4p3u by Molmil](/molmil-images/mine/4p3u) | |
5IX7
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 5ix7 by Molmil](/molmil-images/mine/5ix7) | Crystal structure of metallo-DNA nanowire with infinite one-dimensional silver array | Descriptor: | DNA (5'-D(*GP*GP*AP*CP*TP*(CBR)P*GP*AP*CP*TP*CP*C)-3'), POTASSIUM ION, SILVER ION | Authors: | Kondo, J, Tada, Y, Dairaku, T, Hattori, Y, Saneyoshi, H, Ono, A, Tanaka, Y. | Deposit date: | 2016-03-23 | Release date: | 2017-07-05 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (1.398 Å) | Cite: | A metallo-DNA nanowire with uninterrupted one-dimensional silver array Nat Chem, 9, 2017
|
|
7M3V
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 7m3v by Molmil](/molmil-images/mine/7m3v) | RNA bulged-G motif | Descriptor: | IRIDIUM (III) ION, RNA (27-MER) | Authors: | Kondo, J, Sekiguchi, S. | Deposit date: | 2021-03-19 | Release date: | 2022-03-23 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (2.19 Å) | Cite: | RNA bulged-G motif To Be Published
|
|
4F8U
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 4f8u by Molmil](/molmil-images/mine/4f8u) | Crystal structure of the bacterial ribosomal decoding site in complex with sisomicin (C2 form) | Descriptor: | (1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(aminomethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside, RNA (5'-R(P*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3'), RNA (5'-R(P*UP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3') | Authors: | Kondo, J, Koganei, M, Kasahara, T. | Deposit date: | 2012-05-18 | Release date: | 2012-08-15 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Crystal structure and specific binding mode of sisomicin to the bacterial ribosomal decoding site. Acs Med.Chem.Lett., 3, 2012
|
|
4F8V
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 4f8v by Molmil](/molmil-images/mine/4f8v) | Crystal structure of the bacterial ribosomal decoding site in complex with sisomicin (P21212 form) | Descriptor: | (1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(aminomethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside, RNA (5'-R(P*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3') | Authors: | Kondo, J, Koganei, M, Kasahara, T. | Deposit date: | 2012-05-18 | Release date: | 2012-08-15 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Crystal structure and specific binding mode of sisomicin to the bacterial ribosomal decoding site. Acs Med.Chem.Lett., 3, 2012
|
|
2PWT
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 2pwt by Molmil](/molmil-images/mine/2pwt) | Crystal structure of the bacterial ribosomal decoding site complexed with aminoglycoside containing the L-HABA group | Descriptor: | 22-mer of the ribosomal decoding site, DOUBLY FUNCTIONALIZED PAROMOMYCIN PM-II-162 | Authors: | Kondo, J, Pachamuthu, K, Francois, B, Szychowski, J, Hanessian, S, Westhof, E. | Deposit date: | 2007-05-13 | Release date: | 2007-09-18 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Crystal Structure of the Bacterial Ribosomal Decoding Site Complexed with a Synthetic Doubly Functionalized Paromomycin Derivative: a New Specific Binding Mode to an A-Minor Motif Enhances in vitro Antibacterial Activity Chemmedchem, 2, 2007
|
|
2O3X
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 2o3x by Molmil](/molmil-images/mine/2o3x) | Crystal Structure of the Prokaryotic Ribosomal Decoding Site Complexed with Paromamine Derivative NB30 | Descriptor: | (1R,2R,3S,4R,6S)-4,6-DIAMINO-2-[(5-AMINO-5-DEOXY-BETA-D-RIBOFURANOSYL)OXY]-3-HYDROXYCYCLOHEXYL 2-AMINO-2-DEOXY-ALPHA-D-GLUCOPYRANOSIDE, RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3') | Authors: | Kondo, J, Hainrichson, M, Nudelman, I, Shallom-Shezifi, D, Baasov, T, Westhof, E. | Deposit date: | 2006-12-02 | Release date: | 2007-11-06 | Last modified: | 2023-08-30 | Method: | X-RAY DIFFRACTION (2.9 Å) | Cite: | Differential Selectivity of Natural and Synthetic Aminoglycosides towards the Eukaryotic and Prokaryotic Decoding A Sites. Chembiochem, 8, 2007
|
|
2O3V
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 2o3v by Molmil](/molmil-images/mine/2o3v) | Crystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site complexed with paromamine derivative NB33 | Descriptor: | (2S,3R,4R,5S,6R)-3-AMINO-4-({[(2S,3R,4R,5S,6R)-3-AMINO-2-{[(1R,2R,3S,4R,6S)-4,6-DIAMINO-2,3-DIHYDROXYCYCLOHEXYL]OXY}-5-HYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-4-YL]OXY}METHOXY)-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-2,5-DIOL, RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3') | Authors: | Kondo, J, Hainrichson, M, Nudelman, I, Shallom-Shezifi, D, Baasov, T, Westhof, E. | Deposit date: | 2006-12-02 | Release date: | 2007-11-06 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Differential Selectivity of Natural and Synthetic Aminoglycosides towards the Eukaryotic and Prokaryotic Decoding A Sites. Chembiochem, 8, 2007
|
|
2O3Y
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 2o3y by Molmil](/molmil-images/mine/2o3y) | Crystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site in Presence of Paromamine Derivative NB30 | Descriptor: | RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3'), SPERMINE | Authors: | Kondo, J, Hainrichson, M, Nudelman, I, Shallom-Shezifi, D, Baasov, T, Westhof, E. | Deposit date: | 2006-12-02 | Release date: | 2007-11-06 | Last modified: | 2023-08-30 | Method: | X-RAY DIFFRACTION (2.7 Å) | Cite: | Differential Selectivity of Natural and Synthetic Aminoglycosides towards the Eukaryotic and Prokaryotic Decoding A Sites. Chembiochem, 8, 2007
|
|
2O3W
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 2o3w by Molmil](/molmil-images/mine/2o3w) | Crystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site in presence of paromomycin | Descriptor: | PAROMOMYCIN, RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3') | Authors: | Kondo, J, Hainrichson, M, Nudelman, I, Shallom-Shezifi, D, Baasov, T, Westhof, E. | Deposit date: | 2006-12-02 | Release date: | 2007-11-06 | Last modified: | 2023-08-30 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Differential Selectivity of Natural and Synthetic Aminoglycosides towards the Eukaryotic and Prokaryotic Decoding A Sites. Chembiochem, 8, 2007
|
|
7XLW
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 7xlw by Molmil](/molmil-images/mine/7xlw) | |
4GPX
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 4gpx by Molmil](/molmil-images/mine/4gpx) | Crystal structure of the protozoal cytoplasmic ribosomal decoding site in complex with 6'-hydroxysisomicin (P212121 form) | Descriptor: | (1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(hydroxymethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside, RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3') | Authors: | Kondo, J, Koganei, M, Maianti, J.P, Ly, V.L, Hanessian, S. | Deposit date: | 2012-08-22 | Release date: | 2013-04-03 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Crystal structures of a bioactive 6'-hydroxy variant of sisomicin bound to the bacterial and protozoal ribosomal decoding sites Chemmedchem, 8, 2013
|
|
7BSE
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 7bse by Molmil](/molmil-images/mine/7bse) | |
7BSG
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 7bsg by Molmil](/molmil-images/mine/7bsg) | |
7BSF
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 7bsf by Molmil](/molmil-images/mine/7bsf) | |
7BSH
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 7bsh by Molmil](/molmil-images/mine/7bsh) | |
3TD0
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 3td0 by Molmil](/molmil-images/mine/3td0) | |
7YGP
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 7ygp by Molmil](/molmil-images/mine/7ygp) | DNA duplex containing 5OHU-T base pairs | Descriptor: | COBALT (II) ION, COBALT HEXAMMINE(III), DNA (5'-D(*GP*GP*AP*CP*CP*TP*(OHU)P*GP*GP*TP*CP*C)-3') | Authors: | Kondo, J, Torigoe, H, Arakawa, F. | Deposit date: | 2022-07-12 | Release date: | 2023-05-24 | Last modified: | 2024-05-29 | Method: | X-RAY DIFFRACTION (1.997 Å) | Cite: | Specific binding of Hg 2+ to mismatched base pairs involving 5-hydroxyuracil in duplex DNA. J.Inorg.Biochem., 241, 2023
|
|
7YGO
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 7ygo by Molmil](/molmil-images/mine/7ygo) | DNA duplex containing 5OHU-Hg(II)-T base pairs | Descriptor: | DNA (5'-D(*GP*GP*AP*CP*CP*TP*(6HU)P*GP*GP*TP*CP*C)-3'), MERCURY (II) ION | Authors: | Kondo, J, Torigoe, H, Arakawa, F. | Deposit date: | 2022-07-12 | Release date: | 2023-05-24 | Last modified: | 2024-05-29 | Method: | X-RAY DIFFRACTION (2.403 Å) | Cite: | Specific binding of Hg 2+ to mismatched base pairs involving 5-hydroxyuracil in duplex DNA. J.Inorg.Biochem., 241, 2023
|
|
4P20
![Download](/newweb/media/icons/dl.png) ![Visualize](/newweb/media/icons/hoh_3d.png)
![BU of 4p20 by Molmil](/molmil-images/mine/4p20) | Crystal structures of the bacterial ribosomal decoding site complexed with amikacin | Descriptor: | (2S)-N-[(1R,2S,3S,4R,5S)-4-[(2R,3R,4S,5S,6R)-6-(aminomethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-5-azanyl-2-[(2S,3R,4S,5S ,6R)-4-azanyl-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-2-yl]oxy-3-oxidanyl-cyclohexyl]-4-azanyl-2-oxidanyl-butanamide, 5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3' | Authors: | Kondo, J, Francois, B, Russell, R.J.M, Murray, J.B, Westhof, E. | Deposit date: | 2014-02-28 | Release date: | 2014-05-07 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (2.7 Å) | Cite: | Crystal structure of the bacterial ribosomal decoding site complexed with amikacin containing the gamma-amino-alpha-hydroxybutyryl (haba) group. Biochimie, 88, 2006
|
|