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PDB: 346 results

7RQE
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Crystal structure of the Thermus thermophilus 70S ribosome in complex with protein Y, A-site deacylated tRNA analog CACCA, P-site MAI-tripeptidyl-tRNA analog ACCA-IAM, and chloramphenicol at 2.40A resolution
Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, 16S Ribosomal RNA, 23S Ribosomal RNA, ...
Authors:Syroegin, E.A, Flemmich, L, Klepacki, D, Vazquez-Laslop, N, Micura, R, Polikanov, Y.S.
Deposit date:2021-08-06
Release date:2022-01-26
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Structural basis for the context-specific action of the classic peptidyl transferase inhibitor chloramphenicol.
Nat.Struct.Mol.Biol., 29, 2022
7RQA
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Crystal structure of the Thermus thermophilus 70S ribosome in complex with protein Y, A-site aminoacyl-tRNA analog ACC-PMN, and P-site MTI-tripeptidyl-tRNA analog ACCA-ITM at 2.40A resolution
Descriptor: (4R)-2-METHYLPENTANE-2,4-DIOL, (4S)-2-METHYL-2,4-PENTANEDIOL, 16S Ribosomal RNA, ...
Authors:Syroegin, E.A, Flemmich, L, Klepacki, D, Vazquez-Laslop, N, Micura, R, Polikanov, Y.S.
Deposit date:2021-08-06
Release date:2022-01-26
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Structural basis for the context-specific action of the classic peptidyl transferase inhibitor chloramphenicol.
Nat.Struct.Mol.Biol., 29, 2022
7RQC
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Crystal structure of the Thermus thermophilus 70S ribosome in complex with protein Y, A-site aminoacyl-tRNA analog ACC-PMN, and P-site MFI-tripeptidyl-tRNA analog ACCA-IFM at 2.50A resolution
Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, 16S Ribosomal RNA, 23S Ribosomal RNA, ...
Authors:Syroegin, E.A, Flemmich, L, Klepacki, D, Vazquez-Laslop, N, Micura, R, Polikanov, Y.S.
Deposit date:2021-08-06
Release date:2022-01-26
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Structural basis for the context-specific action of the classic peptidyl transferase inhibitor chloramphenicol.
Nat.Struct.Mol.Biol., 29, 2022
7RQB
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Crystal structure of the Thermus thermophilus 70S ribosome in complex with protein Y, A-site aminoacyl-tRNA analog ACC-PMN, and P-site MAI-tripeptidyl-tRNA analog ACCA-IAM at 2.45A resolution
Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, 16S Ribosomal RNA, 23S Ribosomal RNA, ...
Authors:Syroegin, E.A, Flemmich, L, Klepacki, D, Vazquez-Laslop, N, Micura, R, Polikanov, Y.S.
Deposit date:2021-08-06
Release date:2022-01-26
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2.45 Å)
Cite:Structural basis for the context-specific action of the classic peptidyl transferase inhibitor chloramphenicol.
Nat.Struct.Mol.Biol., 29, 2022
7RQ8
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Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with iboxamycin, mRNA, deacylated A- and E-site tRNAs, and aminoacylated P-site tRNA at 2.50A resolution
Descriptor: 16S Ribosomal RNA, 23S Ribosomal RNA, 30S ribosomal protein S10, ...
Authors:Mitcheltree, M.J, Pisipati, A, Syroegin, E.A, Silvestre, K.J, Klepacki, D, Mason, J.D, Terwilliger, D.W, Testolin, G, Pote, A.R, Wu, K.J.Y, Ladley, R.P, Chatman, K, Mankin, A.S, Polikanov, Y.S, Myers, A.G.
Deposit date:2021-08-06
Release date:2021-10-13
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:A synthetic antibiotic class overcoming bacterial multidrug resistance.
Nature, 599, 2021
7RQ9
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Crystal structure of the A2058-dimethylated Thermus thermophilus 70S ribosome in complex with iboxamycin, mRNA, deacylated A- and E-site tRNAs, and aminoacylated P-site tRNA at 2.60A resolution
Descriptor: 16S Ribosomal RNA, 23S Ribosomal RNA, 30S ribosomal protein S10, ...
Authors:Mitcheltree, M.J, Pisipati, A, Syroegin, E.A, Silvestre, K.J, Klepacki, D, Mason, J.D, Terwilliger, D.W, Testolin, G, Pote, A.R, Wu, K.J.Y, Ladley, R.P, Chatman, K, Mankin, A.S, Polikanov, Y.S, Myers, A.G.
Deposit date:2021-08-06
Release date:2021-10-13
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:A synthetic antibiotic class overcoming bacterial multidrug resistance.
Nature, 599, 2021
3WZJ
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CRYSTAL STRUCTURE OF HUMAN MPS1 CATALYTIC DOMAIN IN COMPLEX WITH 4-(6-(cyclohexylamino)-8-(((tetrahydro-2H-pyran-4-yl)methyl)amino)imidazo[1,2-b]pyridazin-3-yl)-N-cyclopropylbenzamide
Descriptor: 4-{6-(cyclohexylamino)-8-[(tetrahydro-2H-pyran-4-ylmethyl)amino]imidazo[1,2-b]pyridazin-3-yl}-N-cyclopropylbenzamide, Dual specificity protein kinase TTK
Authors:Kusakabe, K, Ide, N, Daigo, Y, Itoh, T, Yamamoto, T, Kojima, E, Mitsuoka, Y, Tadano, G, Tagashira, S, Higashino, K, Okano, Y, Sato, Y, Inoue, M, Iguchi, M, Kanazawa, T, Ishioka, Y, Dohi, K, Kido, Y, Sakamoto, S, Ando, S, Maeda, M, Higaki, M, Yoshizawa, H, Mura, H, Nakamura, Y.
Deposit date:2014-09-29
Release date:2015-02-11
Last modified:2024-05-29
Method:X-RAY DIFFRACTION (2.75 Å)
Cite:Discovery of imidazo[1,2-b]pyridazine derivatives: selective and orally available Mps1 (TTK) kinase inhibitors exhibiting remarkable antiproliferative activity.
J.Med.Chem., 58, 2015
3WZK
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CRYSTAL STRUCTURE OF HUMAN MPS1 CATALYTIC DOMAIN IN COMPLEX WITH N-cyclopropyl-4-(8-((thiophen-2-ylmethyl)amino)imidazo[1,2-a]pyrazin-3-yl)benzamide
Descriptor: CHLORIDE ION, Dual specificity protein kinase TTK, N-cyclopropyl-4-{8-[(thiophen-2-ylmethyl)amino]imidazo[1,2-a]pyrazin-3-yl}benzamide
Authors:Kusakabe, K, Ide, N, Daigo, Y, Itoh, T, Yamamoto, T, Kojima, E, Mitsuoka, Y, Tadano, G, Tagashira, S, Higashino, K, Okano, Y, Sato, Y, Inoue, M, Iguchi, M, Kanazawa, T, Ishioka, Y, Dohi, K, Kido, Y, Sakamoto, S, Ando, S, Maeda, M, Higaki, M, Yoshizawa, H, Mura, H, Nakamura, Y.
Deposit date:2014-09-29
Release date:2015-02-11
Last modified:2024-05-29
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Discovery of imidazo[1,2-b]pyridazine derivatives: selective and orally available Mps1 (TTK) kinase inhibitors exhibiting remarkable antiproliferative activity.
J.Med.Chem., 58, 2015
6XHX
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Crystal structure of the A2058-unmethylated Thermus thermophilus 70S ribosome in complex with erythromycin and protein Y (YfiA) at 2.55A resolution
Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, 16S Ribosomal RNA, 23S Ribosomal RNA, ...
Authors:Svetlov, M.S, Syroegin, E.A, Aleksandrova, E.V, Atkinson, G.C, Gregory, S.T, Mankin, A.S, Polikanov, Y.S.
Deposit date:2020-06-19
Release date:2020-12-23
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2.55 Å)
Cite:Structure of Erm-modified 70S ribosome reveals the mechanism of macrolide resistance.
Nat.Chem.Biol., 17, 2021
5WIS
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Crystal structure of the Thermus thermophilus 70S ribosome in complex with methymycin and bound to mRNA and A-, P- and E-site tRNAs at 2.7A resolution
Descriptor: (3R,4S,5S,7R,9E,11S,12R)-12-ethyl-11-hydroxy-3,5,7,11-tetramethyl-2,8-dioxooxacyclododec-9-en-4-yl 3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranoside, 16S Ribosomal RNA, 23S ribosomal RNA, ...
Authors:Almutairi, M.M, Svetlov, M.S, Hansen, D.A, Khabibullina, N.F, Klepacki, D, Kang, H.Y, Sherman, D.H, Vazquez-Laslop, N, Polikanov, Y.S, Mankin, A.S.
Deposit date:2017-07-20
Release date:2018-02-14
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2.703 Å)
Cite:Co-produced natural ketolides methymycin and pikromycin inhibit bacterial growth by preventing synthesis of a limited number of proteins.
Nucleic Acids Res., 45, 2017
5WIT
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Crystal structure of the Thermus thermophilus 70S ribosome in complex with pikromycin and bound to mRNA and A-, P- and E-site tRNAs at 2.6A resolution
Descriptor: (3R,5R,6S,7S,9R,11E,13S,14R)-14-ethyl-13-hydroxy-3,5,7,9,13-pentamethyl-2,4,10-trioxo-1-oxacyclotetradec-11-en-6-yl 3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranoside, 16S Ribosomal RNA, 23S Ribosomal RNA, ...
Authors:Almutairi, M.M, Svetlov, M.S, Hansen, D.A, Khabibullina, N.F, Klepacki, D, Kang, H.Y, Sherman, D.H, Vazquez-Laslop, N, Polikanov, Y.S, Mankin, A.S.
Deposit date:2017-07-20
Release date:2018-02-14
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Co-produced natural ketolides methymycin and pikromycin inhibit bacterial growth by preventing synthesis of a limited number of proteins.
Nucleic Acids Res., 45, 2017
3WYX
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BU of 3wyx by Molmil
CRYSTAL STRUCTURE OF HUMAN MPS1 CATALYTIC DOMAIN IN COMPLEX WITH 6-((3-(cyanomethoxy)-4-(1-methyl-1H-pyrazol-4-yl)phenyl)amino)-2-(cyclohexylamino)nicotinonitrile
Descriptor: 6-{[3-(cyanomethoxy)-4-(1-methyl-1H-pyrazol-4-yl)phenyl]amino}-2-(cyclohexylamino)pyridine-3-carbonitrile, Dual specificity protein kinase TTK, IODIDE ION
Authors:Kusakabe, K, Ide, N, Daigo, Y, Itoh, T, Yamamoto, T, Kojima, E, Mitsuoka, Y, Tadano, G, Tagashira, S, Higashino, K, Okano, Y, Sato, Y, Inoue, M, Iguchi, M, Kanazawa, T, Ishioka, Y, Dohi, K, Kido, Y, Sakamoto, S, Ando, S, Maeda, M, Higaki, M, Yoshizawa, H, Mura, H, Nakamura, Y.
Deposit date:2014-09-09
Release date:2015-04-08
Last modified:2024-05-29
Method:X-RAY DIFFRACTION (2.9 Å)
Cite:A unique hinge binder of extremely selective aminopyridine-based Mps1 (TTK) kinase inhibitors with cellular activity.
Bioorg.Med.Chem., 23, 2015
7SQO
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Structure of the orexin-2 receptor(OX2R) bound to TAK-925, Gi and scFv16
Descriptor: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2, Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1, Guanine nucleotide-binding protein G(i) subunit alpha-1, ...
Authors:McGrath, A.P, Kang, Y, Flinspach, M.
Deposit date:2021-11-05
Release date:2022-05-25
Last modified:2022-07-06
Method:ELECTRON MICROSCOPY (3.17 Å)
Cite:Molecular mechanism of the wake-promoting agent TAK-925.
Nat Commun, 13, 2022
8CVJ
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Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A-site Phe-NH-tRNAphe, peptidyl P-site fMSEAC-NH-tRNAmet, and deacylated E-site tRNAphe at 2.40A resolution
Descriptor: 16S Ribosomal RNA, 23S Ribosomal RNA, 30S ribosomal protein S10, ...
Authors:Syroegin, E.A, Aleksandrova, E.V, Polikanov, Y.S.
Deposit date:2022-05-18
Release date:2022-10-19
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Insights into the ribosome function from the structures of non-arrested ribosome-nascent chain complexes.
Nat.Chem., 15, 2023
8CVK
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Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A-site Phe-NH-tRNAphe, peptidyl P-site fMRC-NH-tRNAmet, and deacylated E-site tRNAphe at 2.50A resolution
Descriptor: 16S Ribosomal RNA, 23S Ribosomal RNA, 30S ribosomal protein S10, ...
Authors:Syroegin, E.A, Aleksandrova, E.V, Polikanov, Y.S.
Deposit date:2022-05-18
Release date:2022-10-19
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Insights into the ribosome function from the structures of non-arrested ribosome-nascent chain complexes.
Nat.Chem., 15, 2023
8CVL
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Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A-site Phe-NH-tRNAphe, peptidyl P-site fMTHSMRC-NH-tRNAmet, and deacylated E-site tRNAphe at 2.30A resolution
Descriptor: 16S Ribosomal RNA, 23S Ribosomal RNA, 30S ribosomal protein S10, ...
Authors:Syroegin, E.A, Aleksandrova, E.V, Polikanov, Y.S.
Deposit date:2022-05-18
Release date:2022-10-19
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Insights into the ribosome function from the structures of non-arrested ribosome-nascent chain complexes.
Nat.Chem., 15, 2023
8UVR
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BU of 8uvr by Molmil
Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with spectinomycin, mRNA, deacylated A- and E-site tRNAphe, and deacylated P-site tRNAmet at 2.60A resolution
Descriptor: 16S Ribosomal RNA, 23S Ribosomal RNA, 30S ribosomal protein S10, ...
Authors:Killam, B.Y, Phelps, G.A, Lee, R.E, Polikanov, Y.S.
Deposit date:2023-11-03
Release date:2024-08-07
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Development of 2nd generation aminomethyl spectinomycins that overcome native efflux in Mycobacterium abscessus.
Proc.Natl.Acad.Sci.USA, 121, 2024
8UVS
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BU of 8uvs by Molmil
Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with spectinomycin derivative 2694, mRNA, deacylated A- and E-site tRNAphe, and deacylated P-site tRNAmet at 2.75A resolution
Descriptor: (2R,4R,4aS,5aR,6S,7S,8R,9S,9aR,10aS)-2-methyl-6,8-bis(methylamino)-4-({[2-(oxan-4-yl)ethyl]amino}methyl)octahydro-2H-pyrano[2,3-b][1,4]benzodioxine-4,4a,7,9(10aH)-tetrol, 16S Ribosomal RNA, 23S Ribosomal RNA, ...
Authors:Killam, B.Y, Phelps, G.A, Lee, R.E, Polikanov, Y.S.
Deposit date:2023-11-03
Release date:2024-08-07
Method:X-RAY DIFFRACTION (2.75 Å)
Cite:Development of 2nd generation aminomethyl spectinomycins that overcome native efflux in Mycobacterium abscessus.
Proc.Natl.Acad.Sci.USA, 121, 2024
8VTY
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Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with ciprofloxacin and protein Y at 2.60A resolution
Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, 1-CYCLOPROPYL-6-FLUORO-4-OXO-7-PIPERAZIN-1-YL-1,4-DIHYDROQUINOLINE-3-CARBOXYLIC ACID, 16S Ribosomal RNA, ...
Authors:Aleksandrova, E.V, Ma, C.-X, Klepacki, D, Alizadeh, F, Vazquez-Laslop, N, Liang, J.-H, Polikanov, Y.S, Mankin, A.S.
Deposit date:2024-01-27
Release date:2024-08-07
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Macrolones target bacterial ribosomes and DNA gyrase and can evade resistance mechanisms.
Nat.Chem.Biol., 2024
8VTW
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BU of 8vtw by Molmil
Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with macrolone MCX-128 and protein Y at 2.35A resolution
Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, 1-cyclopropyl-7-(4-{4-[({[(3aR,4R,7R,8S,9S,10R,11R,13R,14E,15S,15aR)-10-{[(2S,3R,4S,6R)-4-(dimethylamino)-3-hydroxy-6-methyloxan-2-yl]oxy}-4-ethyl-11-methoxy-14-(methoxyimino)-3a,7,9,11,13,15-hexamethyl-2,6-dioxododecahydro-2H,4H-[1,3]dioxolo[4,5-c]oxacyclotetradecin-8-yl]oxy}carbonyl)amino]butyl}piperazin-1-yl)-6-fluoro-4-oxo-1,4-dihydroquinoline-3-carboxylic acid (non-preferred name), 16S Ribosomal RNA, ...
Authors:Aleksandrova, E.V, Ma, C.-X, Klepacki, D, Alizadeh, F, Vazquez-Laslop, N, Liang, J.-H, Polikanov, Y.S, Mankin, A.S.
Deposit date:2024-01-27
Release date:2024-08-07
Method:X-RAY DIFFRACTION (2.35 Å)
Cite:Macrolones target bacterial ribosomes and DNA gyrase and can evade resistance mechanisms.
Nat.Chem.Biol., 2024
6OMM
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BU of 6omm by Molmil
Cryo-EM structure of formyl peptide receptor 2/lipoxin A4 receptor in complex with Gi
Descriptor: CHOLESTEROL, Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2, Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1, ...
Authors:Zhuang, Y, Liu, H, de Waal, P.W, Zhou, X.E, Wang, L, Meng, X, Zhao, G, Kang, Y, Melcher, K, Xu, H.E, Zhang, C.
Deposit date:2019-04-19
Release date:2020-02-26
Method:ELECTRON MICROSCOPY (3.17 Å)
Cite:Structure of formylpeptide receptor 2-Gicomplex reveals insights into ligand recognition and signaling.
Nat Commun, 11, 2020
7DVO
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BU of 7dvo by Molmil
Structure of Reaction Intermediate of Cytochrome P450 NO Reductase (P450nor) Determined by XFEL
Descriptor: GLYCEROL, NADP nitrous oxide-forming nitric oxide reductase, NITRIC OXIDE, ...
Authors:Nomura, T, Kimura, T, Kanematsu, Y, Yamashita, K, Hirata, K, Ueno, G, Murakami, H, Hisano, T, Yamagiwa, R, Takeda, H, Gopalasingam, C, Yuki, K, Kousaka, R, Yanagasawa, S, Shoji, O, Kumasaka, T, Takano, Y, Ago, H, Yamamoto, M, Sugimoto, H, Tosha, T, Kubo, M, Shiro, Y.
Deposit date:2021-01-14
Release date:2021-05-19
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Short-lived intermediate in N 2 O generation by P450 NO reductase captured by time-resolved IR spectroscopy and XFEL crystallography.
Proc.Natl.Acad.Sci.USA, 118, 2021
8EKB
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Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA, deacylated P-site tRNAmet, and thermorubin at 2.70A resolution
Descriptor: 16S Ribosomal RNA, 23S Ribosomal RNA, 30S ribosomal protein S10, ...
Authors:Paranjpe, M.N, Polikanov, Y.S.
Deposit date:2022-09-20
Release date:2022-12-21
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2.7 Å)
Cite:Insights into the molecular mechanism of translation inhibition by the ribosome-targeting antibiotic thermorubin.
Nucleic Acids Res., 51, 2023
8T8B
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Crystal structure of the Thermus thermophilus 70S ribosome in complex with protein Y, A-site aminoacyl-tRNA analog ACC-PMN, and P-site formyl-MAI-tripeptidyl-tRNA analog ACCA-IAMf at 2.65A resolution
Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, 16S Ribosomal RNA, 23S Ribosomal RNA, ...
Authors:Thaler, J, Syroegin, E.A, Breuker, K, Polikanov, Y.S, Micura, R.
Deposit date:2023-06-22
Release date:2023-07-19
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2.65 Å)
Cite:Practical Synthesis of N -Formylmethionylated Peptidyl-tRNA Mimics.
Acs Chem.Biol., 18, 2023
8T8C
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Crystal structure of the Thermus thermophilus 70S ribosome in complex with protein Y, A-site aminoacyl-tRNA analog ACC-PMN, and P-site formyl-MFI-tripeptidyl-tRNA analog ACCA-IFMf at 2.60A resolution
Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, 16S Ribosomal RNA, 23S Ribosomal RNA, ...
Authors:Thaler, J, Syroegin, E.A, Breuker, K, Polikanov, Y.S, Micura, R.
Deposit date:2023-06-22
Release date:2023-07-19
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Practical Synthesis of N -Formylmethionylated Peptidyl-tRNA Mimics.
Acs Chem.Biol., 18, 2023

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PDB entries from 2024-08-07

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