Structure of a bacterial 50S ribosomal subunit in complex with the novel quinoxolidinone antibiotic cadazolid

2025-12-17 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY STRUCTURE_SUMMARY em_admin entity _chem_comp.name _em_admin.last_update _entity.pdbx_description OTHER atom_sites em_image_scans _atom_sites.fract_transf_matrix[1][1] _atom_sites.fract_transf_matrix[2][2] _atom_sites.fract_transf_matrix[3][3] DATABASE_REFERENCES chem_comp_atom chem_comp_bond database_2 _database_2.pdbx_DOI _database_2.pdbx_database_accession STRUCTURE_SUMMARY atom_site chem_comp chem_comp_atom chem_comp_bond em_admin entity pdbx_entity_nonpoly pdbx_entry_details pdbx_nonpoly_scheme pdbx_unobs_or_zero_occ_atoms struct_site _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.label_atom_id _atom_site.label_comp_id _chem_comp.formula _chem_comp.formula_weight _chem_comp.id _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.type _em_admin.last_update _entity.pdbx_description _pdbx_entity_nonpoly.comp_id _pdbx_entity_nonpoly.name _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _struct_site.details _struct_site.pdbx_auth_comp_id PDBe PDBe 2019-02-27 2019-04-10 2019-04-10 2025-12-17 Structure of a bacterial 50S ribosomal subunit in complex with the novel quinoxolidinone antibiotic cadazolid Scaiola A Leibundgut M ribosome, cadazolid, quinoxolidinone, 50S, ANTIBIOTIC Scaiola A Leibundgut M Boehringer D Caspers P Bur D Locher HH Rueedi G Ritz D Structural basis of translation inhibition by cadazolid, a novel quinoxolidinone antibiotic. Sci Rep UK 9 5634 5634 2019 30948752 doi:10.1038/s41598-019-42155-4 2045-2322 6qul FULLOVERLAP EMDB EMD-4638 associated EM volume

Structure of a bacterial 50S ribosomal subunit in complex with the novel quinoxolidinone antibiotic cadazolid Structure of a bacterial 50S ribosomal subunit in complex with the novel quinoxolidinone antibiotic cadazolid 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 Escherichia coli P-site fMet-tRNA(fMet) Escherichia coli 0.001223818 1 ACCA 23S rRNA Escherichia coli 0.906514125 1 GGUUAAGCGACUAAGCGUACACGGUGGAUGCCCUGGCAGUCAGAGGCGAUGAAGGACGUGCUAAUCUGCGAUAAGCGUCG GUAAGGUGAUAUGAACCGUUAUAACCGGCGAUUUCCGAAUGGGGAAACCCAGUGUGUUUCGACACACUAUCAUUAACUGA AUCCAUAGGUUAAUGAGGCGAACCGGGGGAACUGAAACAUCUAAGUACCCCGAGGAAAAGAAAUCAACCGAGAUUCCCCC AGUAGCGGCGAGCGAACGGGGAGCAGCCCAGAGCCUGAAUCAGUGUGUGUGUUAGUGGAAGCGUCUGGAAAGGCGCGCGA UACAGGGUGACAGCCCCGUACACAAAAAUGCACAUGCUGUGAGCUCGAUGAGUAGGGCGGGACACGUGGUAUCCUGUCUG AAUAUGGGGGGACCAUCCUCCAAGGCUAAAUACUCCUGACUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGCGAAAA GAACCCCGGCGAGGGGAGUGAAAAAGAACCUGAAACCGUGUACGUACAAGCAGUGGGAGCACGCUGGCGUGUGACUGCGU ACCUUUUGUAUAAUGGGUCAGCGACUUAUAUUCUGUAGCAAGGUUAACCGAAUAGGGGAGCCGAAGGGAAACCGAGUCUU AACUGGGCGUUAAGUUGCAGGGUAUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCAGGUUGAAGGUUGGGUAACACUAA CUGGAGGACCGAACCGACUAAUGUUGAAAAAUUAGCGGAUGACUUGUGGCUGGGGGUGAAAGGCCAAUCAAACCGGGAGA UAGCUGGUUCUCCCCGAAAGCUAUUUAGGUAGCGCCUCGUGAAUUCAUCUCCGGGGGUAGAGCACUGUUUCGGCAAGGGG GCUUACCAACCCGAUGCAAACUGCGAAUACCGGAGAAUGUUAUCACGGGAGACACACGGCGGGUGCUAACGUCCGUCGUG AAGAGGGAAACAACCCAGACCGCCAGCUAAGGUCCCAAAGUCAUGGUUAAGUGGGAAACGAUGUGGGAAGGCCCAGACAG CCAGGAUGUUGGCUUAGAAGCAGCCAUCAUUUAAAGAAAGCGUAAUAGCUCACUGGUCGAGUCGGCCUGCGCGGAAGAUG UAACGGGGCUAAACCAUGCACCGAAGCUGCGGCAGCGACGCUGCGUUGUUGGGUAGGGGAGCGUUCUGUAAGCCUGCGAA GGUGUGCUGUGAGGCAUGCUGGAGGUAUCAGAAGUGCGAAUGCUGACAUAAGUAACGAUAAAGCGGGUGAAAAGCCCGCU CGCCGGAAGACCAAGGGUUCCUGUCCAACGUUAAUCGGGGCAGGGUGAGUCGACCCCUAAGGCGAGGCCGAAAGGCGUAG UCGAUGGGAAACAGGUUAAUAUUCCUGUACUUGGUGUUACUGCGAAGGGGGGACGGAGAAGGCUAUGUUGGCCGGGCGAC GGUUGUCCCGGUUUAAGCGUGUAGGCUGGUUUUCCAGGCAAAUCCGGAAAAUCAAGGCUGAGGCGUGAUGACGAGGCGCU GAAGCAACAAAUGCCCUGCUUCCAGGAAAAGCCUCUAAGCAUCAGGUAACAUCAAAUCGUACCCCAAACCGACACAGGUG GUCAGGUAGAGAAUACCAAGGCGCUUGAGAGAACUCGGGUGAAGGAACUAGGCAAAAUGGUGCCGUAACUUCGGGAGAAG GCACGCUGAUAUGUAGGUGAGGUCCCUCGCGGAUGGAGCUGAAAUCAGUCGAAGAUACCAGCUGGCUGCAACUGUUUAUU AAAAACACAGCACUGUGCAAACACGAAAGUGGACGUAUACGGUGUGACGCCUGCCCGGUGCCGGAAGGUUAAUUGAUGGG GUUAGCGCAAGCGAAGCUCUUGAUCGAAGCCCCGGUAAACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCC UUGUCGGGUAAGUUCCGACCUGCACGAAUGGCGUAAUGAUGGCCAGGCUGUCUCCACCCGAGACUCAGUGAAAUUGAACU CGCUGUGAAGAUGCAGUGUACCCGCGGCAAGACGGAAAGACCCCGUGAACCUUUACUAUAGCUUGACACUGAACAUUGAU UGAUGUUCUAACGUUGACCCGUAAUCCGGGUUGCGGACAGUGUCUGGUGGGUAGUUUGACUGGGGCGGUCUCCUCCUAAA GAGUAACGGAGGAGCACGAAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCAGCUUGACU GCGAGCGUGACGGCGCGAGCAGGUGCGAAAGCAGGUCAUAGUGAUCCGGUGGUUCUGAAUGGAAGGGCCAUCGCUCAACG GAUAAAAGGUACUCCGGGGAUAACAGGCUGAUACCGCCCAAGAGUUCAUAUCGACGGCGGUGUUUGGCACCUCGAUGUCG GCUCAUCACAUCCUGGGGCUGAAGUAGGUCCCAAGGGUAUGGCUGUUCGCCAUUUAAAGUGGUACGCGAGCUGGGUUUAG AACGUCGUGAGACAGUUCGGUCCCUAUCUGCCGUGGGCGCUGGAGAACUGAGGGGGGCUGCUCCUAGUACGAGAGGACCG GAGUGGACGCAUCACUGGUGUUCGGGUUGUCAUGCCAAUGGCACUGCCCGGUAGCUAAAUGCGGAAGAGAUAAGUGCUGA AAGCAUCUAAGCACGAAACUUGCCCCGAGAUGAGUUCUCCCUGACCCUUUAAGGGUCCUGAAGGAACGUUGAAGACGACG ACGUUGAUAGGCCGGGUGUGUAAGCGCAGCGAUGCGUUGAGCUAACCGGUACUAAUGAACCGUGAGGCUUAACCU 5S rRNA Escherichia coli 0.03879008999999999 1 UGCCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAACGCCGUAGCGCCGAUGGUAGU GUGGGGUCUCCCCAUGCGAGAGUAGGGAACUGCCAGGCAU CP032237.1 50S ribosomal protein L2 Escherichia coli 0.029923619 1 LEVO MAVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITTRHIGGGHKQAYRIVDFKRNKDGIPAVVER LEYDPNRSANIALVLYKDGERRYILAPKGLKAGDQIQSGVDAAIKPGNTLPMRNIPVGSTVHNVEMKPGKGGQLARSAGT YVQIVARDGAYVTLRLRSGEMRKVEADCRATLGEVGNAEHMLRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNF GKHPVTPWGVQTKGKKTRSNKRTDKFIVRRRSK P60422 50S ribosomal protein L3 Escherichia coli 0.022277534999999998 1 LEVO MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRVTKPEAGHFAKAGVEAGRGLW EFRLAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAGTVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKK MAGQMGNERVTVQSLDVVRVDAERNLLLVKGAVPGATGSDLIVKPAVKA P60438 50S ribosomal protein L4 Escherichia coli 0.022121566 1 LEVO MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPWRQKGTGRARSGSIKSPIWRS GGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIVVEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLA ARNLHKVDVRDATGIDPVSLIAFDKVVMTADAVKQVEEMLA P60723 50S ribosomal protein L5 Escherichia coli 0.020333611 1 LEVO MAKLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLDNAAADLAAISGQKPLITKARKSVAGFKIR QGYPIGCKVTLRGERMWEFFERLITIAVPRIRDFRGLSAKSFDGRGNYSMGVREQIIFPEIDYDKVDRVRGLDITITTTA KSDEEGRALLAAFDFPFRK P62399 50S ribosomal protein L6 Escherichia coli 0.018932791 1 LEVO MSRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKHADNTLTFGPRDGYADGWAQAGTARALLNSMVIGVT EGFTKKLQLVGVGYRAAVKGNVINLSLGFSHPVDHQLPAGITAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGK GVRYADEVVRTKEAKKK P0AG55 50S ribosomal protein L9 Escherichia coli 0.01578902 1 LEVO MQVILLDKVANLGSLGDQVNVKAGYARNFLVPQGKAVPATKKNIEFFEARRAELEAKLAEVLAAANARAEKINALETVTI ASKAGDEGKLFGSIGTRDIADAVTAAGVEVAKSEVRLPNGVLRTTGEHEVSFQVHSEVFAKVIVNVVAE P0A7R1 50S ribosomal protein L13 Escherichia coli 0.016050606 1 LEVO MKTFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNADKVAVTGNKRTDKVYYHHTGH IGGIKQATFEEMIARRPERVIEIAVKGMLPKGPLGRAMFRKLKVYAGNEHNHAAQQPQVLDI P0AA10 50S ribosomal protein L14 Escherichia coli 0.013565066999999998 1 LEVO MIQEQTMLNVADNSGARRVMCIKVLGGSHRRYAGVGDIIKITIKEAIPRGKVKKGDVLKAVVVRTKKGVRRPDGSVIRFD GNACVLLNNNSEQPIGTRIFGPVTRELRSEKFMKIISLAPEVL P0ADY3 50S ribosomal protein L15 Escherichia coli 0.015008470999999999 1 LEVO MRLNTLSPAEGSKKAGKRLGRGIGSGLGKTGGRGHKGQKSRSGGGVRRGFEGGQMPLYRRLPKFGFTSRKAAITAEIRLS DLAKVEGGVVDLNTLKAANIIGIQIEFAKVILAGEVTTPVTVRGLRVTKGARAAIEAAGGKIEE P02413 50S ribosomal protein L16 Escherichia coli 0.015312269 1 LEVO MLQPKRTKFRKMHKGRNRGLAQGTDVSFGSFGLKAVGRGRLTARQIEAARRAMTRAVKRQGKIWIRVFPDKPITEKPLAV RMGKGKGNVEYWVALIQPGKVLYEMDGVPEELAREAFKLAAAKLPIKTTFVTKTVM P0ADY7 50S ribosomal protein L17 Escherichia coli 0.014393656999999999 1 LEVO MRHRKSGRQLNRNSSHRQAMFRNMAGSLVRHEIIKTTLPKAKELRRVVEPLITLAKTDSVANRRLAFARTRDNEIVAKLF NELGPRFASRAGGYTRILKCGFRAGDNAPMAYIELVDRSEKAEAAAE P0AG44 50S ribosomal protein L18 Escherichia coli 0.012794667999999999 1 LEVO MDKKSARIRRATRARRKLQELGATRLVVHRTPRHIYAQVIAPNGSEVLVAASTVEKAIAEQLKYTGNKDAAAAVGKAVAE RALEKGIKDVSFDRSGFQYHGRVQALADAAREAGLQF P0C018 50S ribosomal protein L19 Escherichia coli 0.013159278 1 LEVO MSNIIKQLEQEQMKQDVPSFRPGDTVEVKVWVVEGSKKRLQAFEGVVIAIRNRGLHSAFTVRKISNGEGVERVFQTHSPV VDSISVKRRGAVRKAKLYYLRERTGKAARIKERLN P0A7K6 50S ribosomal protein L20 Escherichia coli 0.013528024 1 LEVO MARVKRGVIARARHKKILKQAKGYYGARSRVYRVAFQAVIKAGQYAYRDRRQRKRQFRQLWIARINAAARQNGISYSKFI NGLKKASVEIDRKILADIAVFDKVAFTALVEKAKAALA P0A7L3 50S ribosomal protein L21 Escherichia coli 0.011586374 1 LEVO MYAVFQSGGKQHRVSEGQTVRLEKLDIATGETVEFAEVLMIANGEEVKIGVPFVDGGVIKAEVVAHGRGEKVKIVKFRRR KHYRKQQGHRQWFTDVKITGISA P0AG48 50S ribosomal protein L22 Escherichia coli 0.012253359 1 LEVO METIAKHRHARSSAQKVRLVADLIRGKKVSQALDILTYTNKKAAVLVKKVLESAIANAEHNDGADIDDLKVTKIFVDEGP SMKRIMPRAKGRADRILKRTSHITVVVSDR P61175 50S ribosomal protein L23 Escherichia coli 0.01122216 1 LEVO MIREERLLKVLRAPHVSEKASTAMEKSNTIVLKVAKDATKAEIKAAVQKLFEVEVEVVNTLVVKGKVKRHGQRIGRRSDW KKAYVTLKEGQNLDFVGGAE P0ADZ0 50S ribosomal protein L24 Escherichia coli 0.011339249999999999 1 LEVO MAAKIRRDDEVIVLTGKDKGKRGKVKNVLSSGKVIVEGINLVKKHQKPVPALNQPGGIVEKEAAIQVSNVAIFNAATGKA DRVGFRFEDGKKVRFFKSNSETIK P60624 50S ribosomal protein L25 Escherichia coli 0.010713465 1 LEVO MFTINAEVRKEQGKGASRRLRAANKFPAIIYGGKEAPLAIELDHDKVMNMQAKAEFYSEVLTIVVDGKEIKVKAQDVQRH PYKPKLQHIDFVRA P68919 50S ribosomal protein L27 Escherichia coli 0.00914654 1 LEVO MAHKKAGGSTRNGRDSEAKRLGVKRFGGESVLAGSIIVRQRGTKFHAGANVGCGRDHTLFAKADGKVKFEVKGPKNRKFI SIEAE P0A7L8 50S ribosomal protein L28 Escherichia coli 0.009027550999999998 1 LEVO MSRVCQVTGKRPVTGNNRSHALNATKRRFLPNLHSHRFWVESEKRFVTLRVSAKGMRVIDKKGIDTVLAELRARGEKY P0A7M2 50S ribosomal protein L29 Escherichia coli 0.0072864639999999994 1 LEVO MKAKELREKSVEELNTELLNLLREQFNLRMQAASGQLQQSHLLKQVRRDVARVKTLLNEKAGA P0A7M6 50S ribosomal protein L30 Escherichia coli 0.006554819999999999 1 LEVO MAKTIKITQTRSAIGRLPKHKATLLGLGLRRIGHTVEREDTPAIRGMINAVSFMVKVEE P0AG51 50S ribosomal protein L32 Escherichia coli 0.006463444999999999 1 LEVO MAVQQNKPTRSKRGMRRSHDALTAVTSLSVDKTSGEKHLRHHITADGYYRGRKVIAK P0A7N4 50S ribosomal protein L33 Escherichia coli 0.006388631 1 LEVO MAKGIREKIKLVSSAGTGHFYTTTKNKRTKPEKLELKKFDPVVRQHVIYKEAKIK P0A7N9 50S ribosomal protein L34 Escherichia coli 0.005397463 1 LEVO MKRTFQPSVLKRNRSHGFRARMATKNGRQVLARRRAKGRARLTVSK P0A7P5 50S ribosomal protein L35 Escherichia coli 0.007313032 1 LEVO MPKIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIACLPYA P0A7Q1 50S ribosomal protein L36 Escherichia coli 0.00437739 1 LEVO MKVRASVKKLCRNCKIVKRDGVIRVICSAEPKHKQRQG P0A7Q6 N-FORMYLMETHIONINE 0.000177221 1 FME MAGNESIUM ION 2.4305e-05 382 MG ADENOSINE MONOPHOSPHATE 0.000347221 1 AMP cadazolid 0.0005855529999999999 1 JJH ZINC ION 6.5409e-05 1 ZN singleParticle particle 7.4 Quantifoil R2/2 COPPER ETHANE-PROPANE 100 277 FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 FEI FALCON II (4k x 4k) INTEGRATING 1.14 1 Gctf PHASE FLIPPING AND AMPLITUDE CORRECTION 4YBB C1 3.0 FSC 0.143 CUT-OFF RELION 3.0 59148 MAXIMUM LIKELIHOOD RELION 2.0 MAXIMUM LIKELIHOOD RELION 3.0 emd_4638.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 290 290 280 0 0 0 290 290 280 312.91 312.91 302.12 90.0 90.0 90.0 X Y Z -0.38431114 0.6159274 0.0015044372 0.025905425 1.079 1.079 1.079 0.1 AUTHOR ::::EMDATABANK.org::::EMD-4638:::: emd_4638_msk_1.map emd_4638_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 431.6 431.6 431.6 90.0 90.0 90.0 X Y Z -0.03499434 0.09757356 0.0002773967 0.006601283 1.079 1.079 1.079 AUTHOR ::::EMDATABANK.org::::EMD-4638:::: emd_4638_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 431.6 431.6 431.6 90.0 90.0 90.0 X Y Z -0.035873875 0.09844687 0.00055442174 0.006603284 1.079 1.079 1.079 AUTHOR ::::EMDATABANK.org::::EMD-4638::::