10PX: Wild-type Thermus thermophilus 70S ribosome
Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with benzoxaborole derivative of azithromycin (AZI-BB2), mRNA, aminoacylated A-site Phe-tRNAphe, aminoacylated P-site fMet-tRNAmet, and deacylated E-site tRNAphe at 2.45A resolution. Determined by X-ray diffraction at 2.45 Å resolution. Released 11 Mar 2026.
- Method
- X-ray diffraction
- Resolution
- 2.45 Å
- Organisms
- Thermus thermophilus HB8, Escherichia phage T4, Escherichia coli
- Chains
- 112
- Atoms
- 300,377
- Mol. weight
- 4573 kDa
- Ligands
- MG, A1C9N, ZN, SF4
- Released
- 11 Mar 2026
Explore 10PX in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
10PX contains 474 α-helices and 654 β-strands across 98 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain 10: 2 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 16-18 | 3 | |
| β-strand | 22-23 | 2 | 176 |
| β-strand | 30-31 | 2 | 177 |
| β-strand | 36-39 | 4 | 176 |
| β-strand | 45-47 | 3 | 177 |
| β-strand | 51-53 | 3 | 176 |
| β-strand | 59-61 | 3 | 176 |
| β-strand | 65-71 | 7 | 177 |
| α-helix | 73-75 | 3 | |
| β-strand | 77-82 | 6 | 177 |
Chain 11: 3 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 13-21 | 9 | 183 |
| α-helix | 25-27 | 3 | |
| β-strand | 33-42 | 10 | 183 |
| β-strand | 46-53 | 8 | 184 |
| β-strand | 56-63 | 8 | 184 |
| α-helix | 68-75 | 8 | |
| α-helix | 87-96 | 10 | |
Chain 12: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-13 | 11 | |
| α-helix | 18-41 | 24 | |
| α-helix | 48-67 | 20 | |
Chain 13: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-8 | 6 | 197 |
| α-helix | 17-25 | 9 | |
| β-strand | 34-38 | 5 | 197 |
| α-helix | 41-49 | 9 | |
| α-helix | 51-53 | 3 | |
| β-strand | 54-59 | 6 | 197 |
Chain 14: 1 helix, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-9 | 4 | |
| β-strand | 10-16 | 7 | 204 |
| β-strand | 21-26 | 6 | 204 |
| β-strand | 30-33 | 4 | 204 |
Chain 15: 4 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-12 | 3 | |
| α-helix | 13-19 | 7 | |
| α-helix | 20-22 | 3 | |
| α-helix | 24-29 | 6 | |
| β-strand | 31-32 | 2 | 1 |
| β-strand | 39-40 | 2 | 1 |
| β-strand | 44 | 1 | 108 |
| β-strand | 51-52 | 2 | 2 |
| β-strand | 55-56 | 2 | 2 |
Chain 16: 1 helix, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-13 | 8 | 6 |
| β-strand | 19-26 | 8 | 6 |
| α-helix | 33-34 | 2 | |
| β-strand | 35-40 | 6 | 6 |
| β-strand | 45-52 | 8 | 6 |
Chain 17: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-16 | 8 | |
| α-helix | 18-22 | 5 | |
| α-helix | 25-36 | 12 | |
90 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| 23S Ribosomal RNA | 1A, 2A | RNA | 2915 | Thermus thermophilus HB8 | |
| 5S Ribosomal RNA | 1B, 2B | RNA | 121 | Thermus thermophilus HB8 | |
| 50S ribosomal protein L2 | 1D, 2D | protein | 276 | Thermus thermophilus HB8 | P60405 (AlphaFold model) |
| 50S ribosomal protein L3 | 1E, 2E | protein | 206 | Thermus thermophilus HB8 | Q5SHN8 (AlphaFold model) |
| 50S ribosomal protein L4 | 1F, 2F | protein | 210 | Thermus thermophilus HB8 | Q5SHN9 (AlphaFold model) |
| 50S ribosomal protein L5 | 1G, 2G | protein | 182 | Thermus thermophilus HB8 | Q5SHQ0 (AlphaFold model) |
| 50S ribosomal protein L6 | 1H, 2H | protein | 180 | Thermus thermophilus HB8 | P0DOY8 |
| 50S ribosomal protein L9 | 1I, 2I | protein | 148 | Thermus thermophilus HB8 | Q5SLQ1 |
| 50S ribosomal protein L13 | 1N, 2N | protein | 140 | Thermus thermophilus HB8 | P60488 |
| 50S ribosomal protein L14 | 1O, 2O | protein | 122 | Thermus thermophilus HB8 | Q5SHP8 |
| 50S ribosomal protein L15 | 1P, 2P | protein | 150 | Thermus thermophilus HB8 | Q5SHQ7 |
| 50S ribosomal protein L16 | 1Q, 2Q | protein | 141 | Thermus thermophilus HB8 | P60489 |
44 more molecules are not listed.
Sequence of entity 1 (1A, 2A), FASTA
>10PX_1 23S Ribosomal RNA (chains 1A, 2A)
GUCAAGAUGGUAAGGGCCCACGGUGGAUGCCUCGGCACCCGAGCCGAUGAAGGACGUGGC
UACCUGCGAUAAGCCAGGGGGAGCCGGUAGCGGGCGUGGAUCCCUGGAUGUCCGAAUGGG
GGAACCCGGCCGGCGGGAACGCCGGUCACCGCGCUUUUGCGCGGGGGGAACCUGGGGAAC
UGAAACAUCUCAGUACCCAGAGGAGAGGAAAGAGAAAUCGACUCCCUGAGUAGCGGCGAG
CGAAAGGGGACCAGCCUAAACCGUCCGGCUUGUCCGGGCGGGGUCGUGGGGCCCUCGGAC
ACCGAAUCCCCAGCCUAGCCGAAGCUGUUGGGAAGCAGCGCCAGAGAGGGUGAAAGCCCC
GUAGGCGAAAGGUGGGGGGAUAGGUGAGGGUACCCGAGUACCCCGUGGUUCGUGGAGCCA
UGGGGGAAUCUGGGCGGACCACCGCCUAAGGCUAAGUACUCCGGGUGACCGAUAGCGCAC
CAGUACCGUGAGGGAAAGGUGAAAAGAACCCCGGGAGGGGAGUGAAAUAGAGCCUGAAAC
CGUGGGCUUACAAGCAGUCACGGCCCCGCAAGGGGUUGUGGCGUGCCUAUUGAAGCAUGA
GCCGGCGACUCACGGUCGUGGGCGAGCUUAAGCCGUUGAGGCGGAGGCGUAGGGAAACCG
AGUCCGAACAGGGCGCAAGCGGGCCGCACGCGGCCCGCAAAGUCCGCGGCCGUGGACCCG
AAACCGGGCGAGCUAGCCCUGGCCAGGGUGAAGCUGGGGUGAGACCCAGUGGAGGCCCGA
ACCGGUGGGGGAUGCAAACCCCUCGGAUGAGCUGGGGCUAGGAGUGAAAAGCUAACCGAG
CCCGGAGAUAGCUGGUUCUCCCCGAAAUGACUUUAGGGUCAGCCUCAGGCGCUGACUGGG
GCCUGUAGAGCACUGAUAGGGCUAGGGGGCCCACCAGCCUACCAAACCCUGUCAAACUCC
GAAGGGUCCCAGGUGGAGCCUGGGAGUGAGGGCGCGAGCGAUAACGUCCGCGUCCGAGCG
CGGGAACAACCGAGACCGCCAGCUAAGGCCCCCAAGUCUGGGCUAAGUGGUAAAGGAUGU
GGCGCCGCGAAGACAGCCAGGAGGUUGGCUUAGAAGCAGCCAUCCUUUAAAGAGUGCGUA
AUAGCUCACUGGUCGAGUGGCGCCGCGCCGAAAAUGAUCGGGGCUUAAGCCCAGCGCCGA
AGCUGCGGGUCUGGGGGAUGACCCCAGGCGGUAGGGGAGCGUUCCCGAUGCCGAUGAAGG
CCGACCCGCGAGGGCGGCUGGAGGUAAGGGAAGUGCGAAUGCCGGCAUGAGUAACGAUAA
AGAGGGUGAGAAUCCCUCUCGCCGUAAGCCCAAGGGUUCCUACGCAAUGGUCGUCAGCGU
AGGGUUAGGCGGGACCUAAGGUGAAGCCGAAAGGCGUAGCCGAAGGGCAGCCGGUUAAUA
UUCCGGCCCUUCCCGCAGGUGCGAUGGGGGGACGCUCUAGGCUAGGGGGACCGGAGCCAU
GGACGAGCCCGGCCAGAAGCGCAGGGUGGGAGGUAGGCAAAUCCGCCUCCCAACAAGCUC
UGCGUGGUGGGGAAGCCCGUACGGGUGACAACCCCCCGAAGCCAGGGAGCCAAGAAAAGC
CUCUAAGCACAACCUGCGGGAACCCGUACCGCAAACCGACACAGGUGGGCGGGUGCAAGA
GCACUCAGGCGCGCGGGAGAACCCUCGCCAAGGAACUCUGCAAGUUGGCCCCGUAACUUC
GGGAGAAGGGGUGCUCCCUGGGGUGAUGAGCCCCGGGGAGCCGCAGUGAACAGGCUCUGG
CGACUGUUUACCAAAAACACAGCUCUCUGCGAACUCGUAAGAGGAGGUAUAGGGAGCGAC
GCUUGCCCGGUGCCGGAAGGUCAAGGGGAGGGGUGCAAGCCCCGAACCGAAGCCCCGGUG
AACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCG
ACCUGCACGAAAAGCGUAACGACCGGAGCGCUGUCUCGGCGAGGGACCCGGUGAAAUUGA
ACUGGCCGUGAAGAUGCGGCCUACCCGUGGCAGGACGAAAAGACCCCGUGGAGCUUUACU
GCAGCCUGGUGUUGGCUCUUGGUCGCGCCUGCGUAGGAUAGGUGGGAGCCUGUGAACCCC
CGCCUCCGGGUGGGGGGGAGGCGCCGGUGAAAUACCACCCUGGCGCGGCUGGGGGCCUAA
CCCUCGGAUGGGGGGACAGCGCUUGGCGGGCAGUUUGACUGGGGCGGUCGCCUCCUAAAA
GGUAACGGAGGCGCCCAAAGGUCCCCUCAGGCGGGACGGAAAUCCGCCGGAGAGCGCAAG
GGUAGAAGGGGGCCUGACUGCGAGGCCUGCAAGCCGAGCAGGGGCGAAAGCCGGGCCUAG
UGAACCGGUGGUCCCGUGUGGAAGGGCCAUCGAUCAACGGAUAAAAGUUACCCCGGGGAU
AACAGGCUGAUCUCCCCCGAGCGUCCACAGCGGCGGGGAGGUUUGGCACCUCGAUGUCGG
CUCGUCGCAUCCUGGGGCUGAAGAAGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCG
GCACGCGAGCUGGGUUCAGAACGUCGUGAGACAGUUCGGUCUCUAUCCGCCACGGGCGCA
GGAGGCUUGAGGGGGGCUCUUCCUAGUACGAGAGGACCGGAAGGGACGCACCUCUGGUUU
CCCAGCUGUCCCUCCAGGGGCAUAAGCUGGGUAGCCAUGUGCGGAAGGGAUAACCGCUGA
AAGCAUCUAAGCGGGAAGCCCGCCCCAAGAUGAGGCCUCCCACGGCGUCAAGCCGGUAAG
GACCCGGGAAGACCACCCGGUGGAUGGGCCGGGGGUGUAAGCGCCGCGAGGCGUUGAGCC
GACCGGUCCCAAUCGUCCGAGGUCUUGACCCCUCC
Sequence of entity 2 (1B, 2B), FASTA
>10PX_2 5S Ribosomal RNA (chains 1B, 2B)
UCCCCCGUGCCCAUAGCGGCGUGGAACCACCCGUUCCCAUUCCGAACACGGAAGUGAAAC
GCGCCAGCGCCGAUGGUACUGGGCGGGCGACCGCCUGGGAGAGUAGGUCGGUGCGGGGGA
U
Sequence of entity 3 (1D, 2D), FASTA
>10PX_3 50S ribosomal protein L2 (chains 1D, 2D)
MAVKKFKPYTPSRRFMTVADFSEITKTEPEKSLVKPLKKTGGRNNQGRITVRFRGGGHKR
LYRIIDFKRWDKVGIPAKVAAIEYDPNRSARIALLHYVDGEKRYIIAPDGLQVGQQVVAG
PDAPIQVGNALPLRFIPVGTVVHAVELEPKKGAKLARAAGTSAQIQGREGDYVILRLPSG
ELRKVHGECYATVGAVGNADHKNIVLGKAGRSRWLGRRPHVRGAAMNPVDHPHGGGEGRA
PRGRPPASPWGWQTKGLKTRKRRKPSSRFIIARRKK
Sequence of entity 4 (1E, 2E), FASTA
>10PX_4 50S ribosomal protein L3 (chains 1E, 2E)
MKGILGVKVGMTRIFRDDRAVPVTVILAGPCPVVQRRTPEKDGYTAVQLGFLPQNPKRVN
RPLKGHFAKAGVEPVRILREIRDFNPEGDTVTVEIFKPGERVDVTGTSKGRGFAGVMKRW
NFAGGPDSHGAHKIHRHPGSIGNRKTPGRVYKGKKMAGHYGAERVTVMNLEVVDVIPEEN
LLLVKGAVPGPNGGLVIVRETKKAAK
Sequence of entity 5 (1F, 2F), FASTA
>10PX_5 50S ribosomal protein L4 (chains 1F, 2F)
MKEVAVYQIPVLSPSGRRELAADLPAEINPHLLWEVVRWQLAKRRRGTASTKTRGEVAYS
GRKIWPQKHTGRARHGDIGAPIFVGGGVVFGPKPRDYSYTLPKKVRKKGLAMAVADRARE
GKLLLVEAFAGVNGKTKEFLAWAKEAGLDGSESVLLVTGNELVRRAARNLPWVVTLAPEG
LNVYDIVRTERLVMDLDAWEVFQNRIGGEA
Sequence of entity 6 (1G, 2G), FASTA
>10PX_6 50S ribosomal protein L5 (chains 1G, 2G)
MPLDVALKRKYYEEVRPELIRRFGYQNVWEVPRLEKVVINQGLGEAKEDARILEKAAQEL
ALITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRMWIFLEKLLNVALPRIRDFRGL
NPNSFDGRGNYNLGLREQLIFPEITYDMVDALRGMDIAVVTTAETDEEARALLELLGFPF
RK
Sequence of entity 7 (1H, 2H), FASTA
>10PX_7 50S ribosomal protein L6 (chains 1H, 2H)
MSRIGRLPIPVPKGVSVEVAPGRVKVKGPKGELEVPVSPEMRVVVEEGVVRVERPSDERR
HKSLHGLTRTLIANAVKGVSEGYSKELLIKGIGYRARLVGRALELTVGFSHPVVVEPPEG
ITFEVPEPTRVRVSGIDKQKVGQVAANIRAIRKPSAYHEKGIYYAGEPVRLKPGKAGAKK
Sequence of entity 8 (1I, 2I), FASTA
>10PX_8 50S ribosomal protein L9 (chains 1I, 2I)
MKVILLEPLENLGDVGQVVDVKPGYARNYLLPRGLAVLATESNLKALEARIRAQAKRLAE
RKAEAERLKEILENLTLTIPVRAGETKIYGSVTAKDIAEALSRQHGVTIDPKRLALEKPI
KELGEYVLTYKPHPEVPIQLKVSVVAQE
Sequence of entity 9 (1N, 2N), FASTA
>10PX_9 50S ribosomal protein L13 (chains 1N, 2N)
MKTYVPKQVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKI
RVTGKKLEQKIYTRYSGYPGGLKKIPLEKMLATHPERVLEHAVKGMLPKGPLGRRLFKRL
KVYAGPDHPHQAQRPEKLEV
Sequence of entity 10 (1O, 2O), FASTA
>10PX_10 50S ribosomal protein L14 (chains 1O, 2O)
MIQPQTYLEVADNTGARKIMCIRVLKGSNAKYATVGDVIVASVKEAIPRGAVKEGDVVKA
VVVRTKKEIKRPDGSAIRFDDNAAVIINNQLEPRGTRVFGPVARELREKGFMKIVSLAPE
VL
Sequence of entity 11 (1P, 2P), FASTA
>10PX_11 50S ribosomal protein L15 (chains 1P, 2P)
MKLSDLRPNPGANKRRKRVGRGPGSGHGKTATRGHKGQKSRSGGLKDPRRFEGGRSTTLM
RLPKRGMQGQVPGEIKRPRYQGVNLKDLARFEGEVTPELLVRAGLLKKGYRLKILGEGEA
KPLKVVAHAFSKSALEKLKAAGGEPVLLEA
Sequence of entity 12 (1Q, 2Q), FASTA
>10PX_12 50S ribosomal protein L16 (chains 1Q, 2Q)
MLMPRRMKYRKQQRGRLKGATKGGDYVAFGDYGLVALEPAWITAQQIEAARVAMVRHFRR
GGKIFIRIFPDKPYTKKPLEVRMGKGKGNVEGYVAVVKPGRVMFEVAGVTEEQAMEALRI
AGHKLPIKTKIVRRDAYDEAQ
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 2794 |
| A1C9N | Azi-BB2 | C52 H85 B N4 O17 | 2 |
| ZN | Zinc ion | Zn | 12 |
| SF4 | Iron/sulfur cluster | Fe4 S4 | 2 |
Water and common crystallization additives (K) are not listed.
Primary citation
Benzoxaborole-modified azithromycins inhibit translation without inducing ermC expression. Volynkina, I.A., Bortyazh, M.O., Chen, C.-.W. et al. Antimicrob Agents Chemother (2026) 70:e0153925-e0153925. DOI 10.1128/aac.01539-25 · PubMed
Other PDB entries of the same protein (UniProt P60405 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 9NO7 2.13 Å, Cryo-EM structure of the wild-type Thermus thermophilus 70S ribosome in complex with…
- 4Y4O 2.3 Å, Crystal structure of the Thermus thermophilus 70S ribosome with rRNA modifications and…
- 8CVL 2.3 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA,…
- 8FC6 2.35 Å, Crystal structure of the A2058-N6-dimethylated Thermus thermophilus 70S ribosome in…
- 8VTW 2.35 Å, Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with…
- 4W2F 2.4 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with amicoumacin,…
- 6XHV 2.4 Å, Crystal structure of the A2058-dimethylated Thermus thermophilus 70S ribosome in complex…
- 7RQA 2.4 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with protein Y,…
- 7RQE 2.4 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with protein Y,…
- 8CVJ 2.4 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA,…
- 8VTU 2.4 Å, Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with…
- 8VTX 2.4 Å, Crystal structure of the A2058-N6-dimethylated Thermus thermophilus 70S ribosome in…
Browse structure collections
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