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8CGD
Clindamycin bound to the 50s subunit
PDB DOI: 10.2210/pdb8cgd/pdb
Classification: RIBOSOME Organism(s): Escherichia Coli Bw25113
Deposited: 2023-02-03 Deposition Author(s): Beckert, B. , Koller, T.O. , Paternoga, H. , Wilson, D.N.
Experimental Data Snapshot
Method: ELECTRON MICROSCOPY Resolution: 1.98 Å
Clindamycin bound to the 50s subunit
Beckert, B. , Koller, T.O. , Paternoga, H. , Wilson, D.N.
Primary Citation of Related Structures: 8CGD
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| Large ribosomal subunit protein bL33 | 0 | 55 | Escherichia Coli Bw25113 | MAKGIREKIKLVSSAGTGHFYTTTKNKRTKPEKLELKKFDPVVRQHVIYKEAKIK |
| Large ribosomal subunit protein uL5 | F | 179 | Escherichia Coli Bw25113 | MAKLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLDNAAADLAAISGQKPLITKARKSVAGFKIRQGYPIGCKVTLRGERMWEFFERLITIAVPRIRDFRGLSAKSFDGRGNYSMGVREQIIFPEIDYDKVDRVRGLDITITTTAKSDEEGRALLAAFDFPFRK |
| Large ribosomal subunit protein uL6 | G | 177 | Escherichia Coli Bw25113 | MSRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKHADNTLTFGPRDGYADGWAQAGTARALLNSMVIGVTEGFTKKLQLVGVGYRAAVKGNVINLSLGFSHPVDHQLPAGITAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGKGVRYADEVVRTKEAKKK |
| Large ribosomal subunit protein bL9 | H | 149 | Escherichia Coli Bw25113 | MQVILLDKVANLGSLGDQVNVKAGYARNFLVPQGKAVPATKKNIEFFEARRAELEAKLAEVLAAANARAEKINALETVTIASKAGDEGKLFGSIGTRDIADAVTAAGVEVAKSEVRLPNGVLRTTGEHEVSFQVHSEVFAKVIVNVVAE |
| Large ribosomal subunit protein uL13 | I | 142 | Escherichia Coli Bw25113 | MKTFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNADKVAVTGNKRTDKVYYHHTGHIGGIKQATFEEMIARRPERVIEIAVKGMLPKGPLGRAMFRKLKVYAGNEHNHAAQQPQVLDI |
| Large ribosomal subunit protein uL14 | J | 123 | Escherichia Coli Bw25113 | MIQEQTMLNVADNSGARRVMCIKVLGGSHRRYAGVGDIIKITIKEAIPRGKVKKGDVLKAVVVRTKKGVRRPDGSVIRFDGNACVLLNNNSEQPIGTRIFGPVTRELRSEKFMKIISLAPEVL |
| 50S ribosomal protein L15 | K | 144 | Escherichia Coli Bw25113 | MRLNTLSPAEGSKKAGKRLGRGIGSGLGKTGGRGHKGQKSRSGGGVRRGFEGGQMPLYRRLPKFGFTSRKAAITAEIRLSDLAKVEGGVVDLNTLKAANIIGIQIEFAKVILAGEVTTPVTVRGLRVTKGARAAIEAAGGKIEE |
| Large ribosomal subunit protein uL16 | L | 136 | Escherichia Coli Bw25113 | MLQPKRTKFRKMHKGRNRGLAQGTDVSFGSFGLKAVGRGRLTARQIEAARRAMTRAVKRQGKIWIRVFPDKPITEKPLAVXXGKGKGNVEYWVALIQPGKVLYEMDGVPEELAREAFKLAAAKLPIKTTFVTKTVM |
| Large ribosomal subunit protein bL17 | M | 127 | Escherichia Coli Bw25113 | MRHRKSGRQLNRNSSHRQAMFRNMAGSLVRHEIIKTTLPKAKELRRVVEPLITLAKTDSVANRRLAFARTRDNEIVAKLFNELGPRFASRAGGYTRILKCGFRAGDNAPMAYIELVDRSEKAEAAAE |
| Large ribosomal subunit protein uL18 | N | 117 | Escherichia Coli Bw25113 | MDKKSARIRRATRARRKLQELGATRLVVHRTPRHIYAQVIAPNGSEVLVAASTVEKAIAEQLKYTGNKDAAAAVGKAVAERALEKGIKDVSFDRSGFQYHGRVQALADAAREAGLQF |
| Large ribosomal subunit protein bL19 | O | 115 | Escherichia Coli Bw25113 | MSNIIKQLEQEQMKQDVPSFRPGDTVEVKVWVVEGSKKRLQAFEGVVIAIRNRGLHSAFTVRKISNGEGVERVFQTHSPVVDSISVKRRGAVRKAKLYYLRERTGKAARIKERLN |
| Large ribosomal subunit protein bL34 | 1 | 46 | Escherichia Coli Bw25113 | MKRTFQPSVLKRNRSHGFRARMATKNGRQVLARRRAKGRARLTVSK |
| Large ribosomal subunit protein bL20 | P | 118 | Escherichia Coli Bw25113 | MARVKRGVIARARHKKILKQAKGYYGARSRVYRVAFQAVIKAGQYAYRDRRQRKRQFRQLWIARINAAARQNGISYSKFINGLKKASVEIDRKILADIAVFDKVAFTALVEKAKAALA |
| Large ribosomal subunit protein bL21 | Q | 103 | Escherichia Coli Bw25113 | MYAVFQSGGKQHRVSEGQTVRLEKLDIATGETVEFAEVLMIANGEEVKIGVPFVDGGVIKAEVVAHGRGEKVKIVKFRRRKHYRKQQGHRQWFTDVKITGISA |
| Large ribosomal subunit protein uL22 | R | 110 | Escherichia Coli Bw25113 | METIAKHRHARSSAQKVRLVADLIRGKKVSQALDILTYTNKKAAVLVKKVLESAIANAEHNDGADIDDLKVTKIFVDEGPSMKRIMPRAKGRADRILKRTSHITVVVSDR |
| Large ribosomal subunit protein uL23 | S | 100 | Escherichia Coli Bw25113 | MIREERLLKVLRAPHVSEKASTAMEKSNTIVLKVAKDATKAEIKAAVQKLFEVEVEVVNTLVVKGKVKRHGQRIGRRSDWKKAYVTLKEGQNLDFVGGAE |
| Large ribosomal subunit protein uL24 | T | 104 | Escherichia Coli Bw25113 | MAAKIRRDDEVIVLTGKDKGKRGKVKNVLSSGKVIVEGINLVKKHQKPVPALNQPGGIVEKEAAIQVSNVAIFNAATGKADRVGFRFEDGKKVRFFKSNSETIK |
| 50S ribosomal protein L25 | U | 94 | Escherichia Coli Bw25113 | MFTINAEVRKEQGKGASRRLRAANKFPAIIYGGKEAPLAIELDHDKVMNMQAKAEFYSEVLTIVVDGKEIKVKAQDVQRHPYKPKLQHIDFVRA |
| Large ribosomal subunit protein bL27 | V | 85 | Escherichia Coli Bw25113 | MAHKKAGGSTRNGRDSEAKRLGVKRFGGESVLAGSIIVRQRGTKFHAGANVGCGRDHTLFAKADGKVKFEVKGPKNRKFISIEAE |
| Large ribosomal subunit protein bL28 | W | 78 | Escherichia Coli Bw25113 | MSRVCQVTGKRPVTGNNRSHALNATKRRFLPNLHSHRFWVESEKRFVTLRVSAKGMRVIDKKGIDTVLAELRARGEKY |
| Large ribosomal subunit protein uL29 | X | 63 | Escherichia Coli Bw25113 | MKAKELREKSVEELNTELLNLLREQFNLRMQAASGQLQQSHLLKQVRRDVARVKTLLNEKAGA |
| Large ribosomal subunit protein uL30 | Y | 59 | Escherichia Coli Bw25113 | MAKTIKITQTRSAIGRLPKHKATLLGLGLRRIGHTVEREDTPAIRGMINAVSFMVKVEE |
| Large ribosomal subunit protein bL35 | 2 | 65 | Escherichia Coli Bw25113 | MPKIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIACLPYA |
| Large ribosomal subunit protein bL32 | Z | 57 | Escherichia Coli Bw25113 | MAVQQNKPTRSKRGMRRSHDALTAVTSLSVDKTSGEKHLRHHITADGYYRGRKVIAK |
| Large ribosomal subunit protein bL36A | 3 | 38 | Escherichia Coli Bw25113 | MKVRASVKKLCRNCKIVKRDGVIRVICSAEPKHKQRQG |
| Large ribosomal subunit protein uL2 | C | 273 | Escherichia Coli Bw25113 | MAVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITTRHIGGGHKQAYRIVDFKRNKDGIPAVVERLEYDPNRSANIALVLYKDGERRYILAPKGLKAGDQIQSGVDAAIKPGNTLPMRNIPVGSTVHNVEMKPGKGGQLARSAGTYVQIVARDGAYVTLRLRSGEMRKVEADCRATLGEVGNAEHMLRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNFGKHPVTPWGVQTKGKKTRSNKRTDKFIVRRRSK |
| Large ribosomal subunit protein uL3 | D | 209 | Escherichia Coli Bw25113 | MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRVTKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAGTVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVRVDAERNLLLVKGAVPGATGSDLIVKPAVKA |
| Large ribosomal subunit protein uL4 | E | 201 | Escherichia Coli Bw25113 | MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPWRQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIVVEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLAARNLHKVDVRDATGIDPVSLIAFDKVVMTADAVKQVEEMLA |
| Nucleic Acids / Hybrid | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 23S rRNA | a | 2904 | NA | GGUUAAGCGACUAAGCGUACACGGUGGAUGCCCUGGCAGUCAGAGGCGAUGAAGGACGUGCUAAUCUGCGAUAAGCGUCGGUAAGGUGAUAUGAACCGUUAUAACCGGCGAUUUCCGAAUGGGGAAACCCAGUGUGUUUCGACACACUAUCAUUAACUGAAUCCAUAGGUUAAUGAGGCGAACCGGGGGAACUGAAACAUCUAAGUACCCCGAGGAAAAGAAAUCAACCGAGAUUCCCCCAGUAGCGGCGAGCGAACGGGGAGCAGCCCAGAGCCUGAAUCAGUGUGUGUGUUAGUGGAAGCGUCUGGAAAGGCGCGCGAUACAGGGUGACAGCCCCGUACACAAAAAUGCACAUGCUGUGAGCUCGAUGAGUAGGGCGGGACACGUGGUAUCCUGUCUGAAUAUGGGGGGACCAUCCUCCAAGGCUAAAUACUCCUGACUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGCGAAAAGAACCCCGGCGAGGGGAGUGAAAAAGAACCUGAAACCGUGUACGUACAAGCAGUGGGAGCACGCUUAGGCGUGUGACUGCGUACCUUUUGUAUAAUGGGUCAGCGACUUAUAUUCUGUAGCAAGGUUAACCGAAUAGGGGAGCCGAAGGGAAACCGAGUCUUAACUGGGCGUUAAGUUGCAGGGUAUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCAGGUUGAAGGUUGGGUAACACUAACUGGAGGACCGAACCGACUAAUGUUGAAAAAUUAGCGGAUGACUUGUGGCUGGGGGUGAAAGGCCAAUCAAACCGGGAGAUAGCUGGUUCUCCCCGAAAGCUAUUUAGGUAGCGCCUCGUGAAUUCAUCUCCGGGGGUAGAGCACUGUUUCGGCAAGGGGGUCAUCCCGACUUACCAACCCGAUGCAAACUGCGAAUACCGGAGAAUGUUAUCACGGGAGACACACGGCGGGUGCUAACGUCCGUCGUGAAGAGGGAAACAACCCAGACCGCCAGCUAAGGUCCCAAAGUCAUGGUUAAGUGGGAAACGAUGUGGGAAGGCCCAGACAGCCAGGAUGUUGGCUUAGAAGCAGCCAUCAUUUAAAGAAAGCGUAAUAGCUCACUGGUCGAGUCGGCCUGCGCGGAAGAUGUAACGGGGCUAAACCAUGCACCGAAGCUGCGGCAGCGACGCUUAUGCGUUGUUGGGUAGGGGAGCGUUCUGUAAGCCUGCGAAGGUGUGCUGUGAGGCAUGCUGGAGGUAUCAGAAGUGCGAAUGCUGACAUAAGUAACGAUAAAGCGGGUGAAAAGCCCGCUCGCCGGAAGACCAAGGGUUCCUGUCCAACGUUAAUCGGGGCAGGGUGAGUCGACCCCUAAGGCGAGGCCGAAAGGCGUAGUCGAUGGGAAACAGGUUAAUAUUCCUGUACUUGGUGUUACUGCGAAGGGGGGACGGAGAAGGCUAUGUUGGCCGGGCGACGGUUGUCCCGGUUUAAGCGUGUAGGCUGGUUUUCCAGGCAAAUCCGGAAAAUCAAGGCUGAGGCGUGAUGACGAGGCACUACGGUGCUGAAGCAACAAAUGCCCUGCUUCCAGGAAAAGCCUCUAAGCAUCAGGUAACAUCAAAUCGUACCCCAAACCGACACAGGUGGUCAGGUAGAGAAUACCAAGGCGCUUGAGAGAACUCGGGUGAAGGAACUAGGCAAAAUGGUGCCGUAACUUCGGGAGAAGGCACGCUGAUAUGUAGGUGAGGUCCCUCGCGGAUGGAGCUGAAAUCAGUCGAAGAUACCAGCUGGCUGCAACUGUUUAUUAAAAACACAGCACUGUGCAAACACGAAAGUGGACGUAUACGGUGUGACGCCUGCCCGGUGCCGGAAGGUUAAUUGAUGGGGUUAGCGCAAGCGAAGCUCUUGAUCGAAGCCCCGGUAAACGGCGGCCGUAACXAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAUGGCGUAAUGAUGGCCAGGCUGUCUCCACCCGAGACUCAGUGAAAUUGAACUCGCUGUGAAGAUGCAGUGUACCCGCGGCAAGACGGAAAGACCCCGUGAACCUUUACUAUAGCUUGACACUGAACAUUGAGCCUUGAUGUGUAGGAUAGGUGGGAGGCUUUGAAGUGUGGACGCCAGUCUGCAUGGAGCCGACCUUGAAAUACCACCCUUUAAUGUUUGAUGUUCUAACGUUGACCCGUAAUCCGGGUUGCGGACAGUGUCUGGUGGGUAGUUUGACUGGGGCGGUCUCCUCCUAAAGAGUAACGGAGGAGCACGAAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCAGCUUGACUGCGAGCGUGACGGCGCGAGCAGGUGCGAAAGCAGGUCAUAGUGAUCCGGUGGUUCUGAAUGGAAGGGCCAUCGCUCAACGGAUAAAAGGUACUCCGGGGAUAACAGGCUGAUACCGCCCAAGAGUUCAUAUCGACGGCGGUGUUUGGCACCUCGAUGUCGGCUCAUCACAUCCUGGGGCUGAAGUAGGUCCCAAGGGUAUGGCUGUUCGCCAUUUAAAGUGGUACGCGAGCUGGGUUUAGAACGUCGUGAGACAGUUCGGUCCCUAUCUGCCGUGGGCGCUGGAGAACUGAGGGGGGCUGCUCCUAGUACGAGAGGACCGGAGUGGACGCAUCACUGGUGUUCGGGUUGUCAUGCCAAUGGCACUGCCCGGUAGCUAAAUGCGGAAGAGAUAAGUGCUGAAAGCAUCUAAGCACGAAACUUGCCCCGAGAUGAGUUCUCCCUGACCCUUUAAGGGUCCUGAAGGAACGUUGAAGACGACGACGUUGAUAGGCCGGGUGUGUAAGCGCAGCGAUGCGUUGAGCUAACCGGUACUAAUGAACCGUGAGGCUUAACCUU |
| 5S rRNA | b | 120 | NA | UGCCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAACGCCGUAGCGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGGAACUGCCAGGCAU |
Experimental Data
Method: ELECTRON MICROSCOPY
Deposited Date: 2023-02-03 Deposition Author(s): Beckert, B. , Koller, T.O. , Paternoga, H. , Wilson, D.N.