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5DM7
Crystal structure of the 50s ribosomal subunit from deinococcus radiodurans in complex with hygromycin a
PDB DOI: 10.2210/pdb5dm7/pdb
Classification: RIBOSOME Organism(s): Deinococcus Radiodurans
Deposited: 2015-09-08 Deposition Author(s): Connell, S.R. , Fucini, P. , Kaminishi, T. , Ochoa-Lizarralde, B. , Schedlbauer, A.
Experimental Data Snapshot
Method: X-RAY DIFFRACTION Resolution: 3 Å
Crystal structure of the 50s ribosomal subunit from deinococcus radiodurans in complex with hygromycin a
Connell, S.R. , Fucini, P. , Kaminishi, T. , Ochoa-Lizarralde, B. , Schedlbauer, A.
Primary Citation of Related Structures: 5DM7
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 50S ribosomal protein L1 | 0 | 224 | Deinococcus Radiodurans | KRYRALEGKVDRNKQYSIDEAAALVKELATAKFDETVEVHFRLGIDPRKSDQNVRGTVALPHGTGRSVRVAVITKGENVQAAEAAGADVVGSDELIERIAGGFMDFDAVVATPDMMAQIGQKLARLLGPRGLLPNPKSGTVGADVAGMVRGLKAGRIEFRNDKTGVVHAPIGKASFESGNLSANYQALISALEGAKPGTAKGVFLRSAYLTTTMGPSIPLALGG |
| 50S ribosomal protein L15 | I | 141 | Deinococcus Radiodurans | HDLKPTPGSRKDRKRVGRGPGGTDKTAGRGHKGQKSRSGAGKGAFFEGGRSRLIARLPKRGFNNVGTTYEVVKLSQLQDLEDTTFDRDTLEAYRLVRRKNRPVKLLASGEISRAVTVHVDAASAAAIKAVEAAGGRVVLPE |
| 50S ribosomal protein L16 | J | 136 | Deinococcus Radiodurans | KRTKFRKQFRGRMTGDAKGGDYVAFGDYGLIAMEPAWIKSNQIEACRIVMSRHFRRGGKIYIRIFPDKPVTKKPAETRMGKGKGAVEYWVSVVKPGRVMFEVAGVTEEQAKEAFRLAGHKLPIQTKMVKREVYDEA |
| 50S ribosomal protein L17 | K | 113 | Deinococcus Radiodurans | HGKAGRKLNRNSSARVALARAQATALLREGRIQTTLTKAKELRPFVEQLITTAKGGDLHSRRLVAQDIHDKDVVRKVMDEVAPKYAERPGGYTRILRVGTRRGDGVTMALIEL |
| 50S ribosomal protein L18 | L | 104 | Deinococcus Radiodurans | RRKLRTRRKVRTTTAASGKLRLSVYRSSKHIYAQIIDDSRGQTLAAASSAALKSGNKTDTAAAVGKALAAAAAEKGIKQVVFDRGSYKYHGRVKALADAAREGG |
| 50S ribosomal protein L19 | M | 109 | Deinococcus Radiodurans | QTHIKINRGELLRGIEQDHTRQLPDFRPGDTVRVDTKVREGNRTRSQAFEGVVIAINGSGSRKSFTVRKISFGEGVERVFPFASPLVNQVTIVERGKVRRAKLYYGKAA |
| 50S ribosomal protein L20 | N | 117 | Deinococcus Radiodurans | PRAKTGIVRRRRHKKVLKRAKGFWGSRSKQYRNAFQTLLNAATYEYRDRRNKKRDFRRLWIQRINAGARLHGMNYSTFINGLKRANIDLNRKVLADIAAREPEAFKALVDASRNARQ |
| 50S ribosomal protein L21 | O | 94 | Deinococcus Radiodurans | IQTGGKQYRVSEGDVIRVESLQGEAGDKVELKALFVGGEQTVFGEDAGKYTVQAEVVEHGRGKKIYIRKYKSGVQYRRRTGHRQNFTAIKILGI |
| 50S ribosomal protein L22 | P | 127 | Deinococcus Radiodurans | FRNKKQRKQQVKLRKPGFAVAKYVRMSPRKVRLVVDVIRGKSVQDAEDLLRFIPRSASEPVAKVLNSAKANALHNDEMLEDRLFVKEAYVDAGPTLKRLIPRARGSANIIKKRTSHITIIVAEKGNK |
| 50S ribosomal protein L23 | Q | 93 | Deinococcus Radiodurans | SHYDILQAPVISEKAYSAMERGVYSFWVSPKATKTEIKDAIQQAFGVRVIGISTMNVPGKRKRVGRFIGQRNDRKKAIVRLAEGQSIEALAGQ |
| 50S ribosomal protein L24 | R | 110 | Deinococcus Radiodurans | PSAGSHHNDKLHFKKGDTVIVLSGKHKGQTGKVLLALPRDQKVVVEGVNVITKNVKPSMTNPQGGQEQRELALHASKVALVDPETGKATRVRKQIVDGKKVRVAVASGKT |
| 50S ribosomal protein L2 | A | 274 | Deinococcus Radiodurans | AVKKYKPYTPSRRQMTTADFSGLAKKRPEKALTEALPKTGGRNNRGRITSRFIGGGHKRLYRIIDFKRRDKSGVNAKVAAIEYDPNRSARIALLHYADGEKRYILAPEGLTVGATVNAGPEAEPKLGNALPLRFVPVGAVVHALELVPGKGAQLARSAGTSVQVQGKESDYVIVRLPSGELRRVHSECYATIGAVGNAEHKNIVLGKAGRSRWLGRKPHQRGSAMNPVDHPHGGGEGRTGAGRVPVTPWGKPTKGLKTRRKRKTSDRFLVTRRK |
| 50S ribosomal protein L25 | S | 175 | Deinococcus Radiodurans | MELTAKPRTPKQKLDESMIAAVAYNKENNVSFALDRKAFDRAFRQQSTTGLFDITVEGGETFPALVKAVQMDKRKRAPIHVDFYMVTYGEPVEVSVPVHTTGRSQGEVQGGLVDIVVHNLQIVAPGPRRIPQELVVDVTKMNIGDHITAGDIKLPEGCTLAADPELTVVSVLPPR |
| 50S ribosomal protein L27 | T | 84 | Deinococcus Radiodurans | AHKKGVGSSKNGRDSNPKYLGVKKFGGEVVKAGNILVRQRGTKFKAGQGVGMGRDHTLFALSDGKVVFINKGKGARFISIEAAQ |
| 50S ribosomal protein L28 | U | 72 | Deinococcus Radiodurans | TGKKNLVVNSVIRRGKARADGGVGRKTTGITKRVQRANLHKKAIRENGQVKTVWLSANAIRTLSKGPYKGIE |
| 50S ribosomal protein L29 | V | 66 | Deinococcus Radiodurans | MKPSEMRNLQATDFAKEIDARKKELMELRFQAAAGQLAQPHRVRQLRREVAQLNTVKAELARKGEQ |
| 50S ribosomal protein L30 | W | 55 | Deinococcus Radiodurans | MKIKLVRSVIGRPGNQVKTVQALGLRKIGDSREVSDTPAVRGMVKTVKHLLEVQE |
| 50S ribosomal protein L32 | Z | 57 | Deinococcus Radiodurans | KHPVPKKKTSKSKRDMRRSHHALTAPNLTECPQCHGKKLSHHICPNCGYYDGRQVLA |
| 50S ribosomal protein L33 | 1 | 54 | Deinococcus Radiodurans | AAAGAAPRIIVKMESSAGTGFYYTTTKNRRNTQAKLELKKYDPVAAHVVFAAAA |
| 50S ribosomal protein L34 | 2 | 47 | Deinococcus Radiodurans | MKRTYQPNNRKRAKTHGFRARMKTKSGRNILARRRAKGRHQLTVSDE |
| 50S ribosomal protein L35 | 3 | 65 | Deinococcus Radiodurans | PKMKTHKMAKRRIKITGTGKVMAFKSGKRHQNTGKSGDEIRGKGKGFVLAKAEWARMKLMLPRGK |
| 50S ribosomal protein L3 | B | 205 | Deinococcus Radiodurans | MKGILGTKIGMTQIWKNDRAIPVTVVLAGPCPIVQRKTAQTDGYEAVQIGYAPKAERKVNKPMQGHFAKAGVAPTRILREFRGFAPDGDSVNVDIFAEGEKIDATGTSKGKGTQGVMKRWNFAGGPASHGSKKWHRRPGSIGQRKTPGRVYKGKRMAGHMGMERVTVQNLEVVEIRAGENLILVKGAIPGANGGLVVLRSAAKAS |
| 50S ribosomal protein L4 | C | 197 | Deinococcus Radiodurans | AQINVIGQNGGRTIELPLPEVNSGVLHEVVTWQLASRRRGTASTRTRAQVSKTGRKMYGQKGTGNARHGDRSVPTFVGGGVAFGPKPRSYDYTLPRQVRQLGLAMAIASRQEGGKLVAVDGFDIADAKTKNFISWAKQNGLDGTEKVLLVTDDENTRRAARNVSWVSVLPVAGVNVYDILRHDRLVIDAAALEIVEE |
| 50S ribosomal protein L5 | D | 177 | Deinococcus Radiodurans | QLKTKYNDQVRPALMQQFGYSSVMAVPRIEKIVVNEGLGSSKEDSKAIDKAAKELALITLQKPIITKAKKSISNFKLRQGMPVGIKVTLRGERMYVFLEKLINIGLPRIRDFRGINPNAFDGRGNYNLGIKEQLIFPEITYDMVDKTRGMDITIVTTAKTDEEARALLQSMGLPFRK |
| 50S ribosomal protein L6 | E | 171 | Deinococcus Radiodurans | GKQPIAVPSGVTVNAQDGVFKVKGPKGELTVPYNTELTVRQDGDQLLVERPSDAQKHRALHGLTRTLVANAVKGVSDGYTINLELRGVGFRAKLTGKALEMNIGYSHPVIIEPPAGVTFAVPEPTRIDVSGIDKQLVGQVAANVRKVRKPDAYHGKGVRFVGEQIALKAGK |
| 50S ribosomal protein L11 | F | 144 | Deinococcus Radiodurans | MRRVAGIVKLQLPAGKATPAPPVGPALGQYGANIMEFTKAFNAQTADKGDAIIPVEITIYADRSFTFITKTPPMSYLIRKAAGIGKGSSTPNKAKVGKLNWDQVLEIAKTKMPDLNAGSVEAAANTVAGTARSMGVTVEGGPNA |
| 50S ribosomal protein L13 | G | 142 | Deinococcus Radiodurans | KTYIPKNDEQNWVVVDASGVPLGRLATLIASRIRGKHRPDFTPNMIQGDFVVVINAAQVALTGKKLDDKVYTRYTGYQGGLKTETAREALSKHPERVIEHAVFGMLPKGRQGRAMHTRLKVYAGETHPHSAQKPQVLKTQPL |
| 50S ribosomal protein L14 | H | 134 | Deinococcus Radiodurans | MIMPQSRLDVADNSGAREIMCIRVLNSGIGGKGLTTGGGGNKRYAHVGDIIVASVKDAAPRGAVKAGDVVKAVVVRTSHAIKRADGSTIRFDRNAAVIINNQGEPRGTRVFGPVARELRDRRFMKIVSLAPEVL |
| Nucleic Acids / Hybrid | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 23S ribosomal RNA | x | 2881 | NA | GGGUCAAGAUAGUAAGGGUCCACGGUGGAUGCCCUGGCGCUGGAGCCGAUGAAGGACGCGAUUACCUGCGAAAAGCCCCGACGAGCUGGAGAUACGCUUUGACUCGGGGAUGUCCGAAUGGGGAAACCCACCUCGUAAGAGGUAUCCGCAAGGAUGGGAACUCAGGGAACUGAAACAUCUCAGUACCUGAAGGAGAAGAAAGAGAAUUCGAUUCCGUUAGUAGCGGCGAGCGAACCCGGAUCAGCCCAAACCGAAACGCUUGCGUUUCGGGGUUGUAGGACCAGUUUUUAAGAUUCAACCCCUCAAGCCGAAGUGGCUGGAAAGCUACACCUCAGAAGGUGAGAGUCCUGUAGGCGAACGAGCGGUUGACUGUACUGGCACCUGAGUAGGUCGUUGUUCGUGAAACGAUGACUGAAUCCGCGCGGACCACCGCGCAAGGCUAAAUACUCCCAGUGACCGAUAGCGCAUAGUACCGUGAGGGAAAGGUGAAAAGAACCCCGGGAGGGGAGUGAAAGAGAACCUGAAACCGUGGACUUACAAGCAGUCAUGGCACCUUAUGCGUGUUAUGGCGUGCCUAUUGAAGCAUGAGCCGGCGACUUAGACCUGACGUGCGAGCUUAAGUUGAAAAACGGAGGCGGAGCGAAAGCGAGUCCGAAUAGGGCGGCAUUAGUACGUCGGGCUAGACUCGAAACCAGGUGAGCUAAGCAUGACCAGGUUGAAACCCCCGUGACAGGGGGCGGAGGACCGAACCGGUGCCUGCUGAAACAGUCUCGGAUGAGUUGUGUUUAGGAGUGAAAAGCUAACCGAACCUGGAGAUAGCUAGUUCUCCCCGAAAUGUAUUGAGGUACAGCCUCGGAUGUUGACCAUGUCCUGUAGAGCACUCACAAGGCUAGGGGGCCUACCAGCUUACCAAACCUUAUGAAACUCCGAAGGGGCACGCGUUUAGUCCGGGAGUGAGGCUGCGAGAGCUAACUUCCGUAGCCGAGAGGGAAACAACCCAGACCAUCAGCUAAGGUCCCUAAAUGAUCGCUCAGUGGUUAAGGAUGUGUCGUCGCAUAGACAGCCAGGAGGUUGGCUUAGAAGCAGCCACCCUUCAAAGAGUGCGUAAUAGCUCACUGGUCGAGUGACGAUGCGCCGAAAAUGAUCGGGGCUCAAGUGAUCUACCGAAGCUAUGGAUUCAACUCGCGAAGCGAGUUGUCUGGUAGGGGAGCGUUCAGUCCGCGGAGAAGCCAUACCGGAAGGAGUGGUGGAGCCGACUGAAGUGCGGAUGCCGGCAUGAGUAACGAUAAAAGAAGUGAGAAUCUUCUUCGCCGUAAGGACAAGGGUUCCUGGGGAAGGGUCGUCCGCCCAGGGAAAGUCGGGACCUAAGGUGAGGCCGAACGGCGCAGCCGAUGGACAGCAGGUCAAGAUUCCUGCACCGAUCAUGUGGAGUGAUGGAGGGACGCAUUACGCUAUCCAAUGCCAAGCUAUGGCUAUGCUGGUUGGUACGCUCAAGGGCGAUCGGGUCAGAAAAUCUACCGGUCACAUGCCUCAGACGUAUCGGGAGCUUCCUCGGAAGCGAAGUUGGAAACGCGACGGUGCCAAGAAAAGCUUCUAAACGUUGAAACAUGAUUGCCCGUACCGCAAACCGACACAGGUGUCCGAGUGUCAAUGCACUAAGGCGCGCGAGAGAACCCUCGUUAAGGAACUUUGCAAUCUCACCCCGUAACUUCGGAAGAAGGGGUCCCCACGCUUCGCGUGGGGCGCAGUGAAUAGGCCCAGGCGACUGUUUACCAAAAUCACAGCACUCUGCCAACACGAACAGUGGACGUAUAGGGUGUGACGCCUGCCCGGUGCCGGAAGGUCAAGUGGAGCGGUGCAAGCUGCGAAAUGAAGCCCCGGUGAACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAAGGCGUAACGAUCUGGGCGCUGUCUCAACGAGGGACUCGGUGAAAUUGAAUUGGCUGUAAAGAUGCGGCCUACCCGUAGCAGGACGAAAAGACCCCGUGGAGCUUUACUAUAGUCUGGCAUUGGGAUUCGGGUUUCUCUGCGUAGGAUAGGUGGGAGCCUGCGAAACUGGCCUUUUGGGGUCGGUGGAGGCAACGGUGAAAUACCACCCUGAGAAACUUGGAUUUCUAACCUGAAAAAUCACUUUCGGGGACCGUGCUUGGCGGGUAGUUUGACUGGGGCGGUCGCCUCCCAAAAUGUAACGGAGGCGCCCAAAGGUCACCUCAAGACGGUUGGAAAUCGUCUGUAGAGCGCAAAGGUAGAAGGUGGCUUGACUGCGAGACUGACACGUCGAGCAGGGAGGAAACUCGGGCUUAGUGAACCGGUGGUACCGUGUGGAAGGGCCAUCGAUCAACGGAUAAAAGUUACCCCGGGGAUAACAGGCUGAUCUCCCCCGAGAGUCCAUAUCGGCGGGGAGGUUUGGCACCUCGAUGUCGGCUCGUCGCAUCCUGGGGCUGAAGAAGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCGGCACGCGAGCUGGGUUCAGAACGUCGUGAGACAGUUCGGUCUCUAUCCGCUACGGGCGCAGGAGAAUUGAGGGGAGUUGCUCCUAGUACGAGAGGACCGGAGUGAACGGACCGCUGGUCUCCCUGCUGUCGUACCAACGGCACAUGCAGGGUAGCUAUGUCCGGAACGGAUAACCGCUGAAAGCAUCUAAGCGGGAAGCCAGCCCCAAGAUGAGUUCUCCCACUGUUUAUCAGGUAAGACUCCCGGAAGACCACCGGGUUAAGAGGCCAGGCGUGCACGCAUAGCAAUGUGUUCAGCGGACUGGUGCUCAUCAGUCGAGGUCUUGACCACUC |
| 5S ribosomal RNA | y | 122 | NA | CACCCCCGUGCCCAUAGCACUGUGGAACCACCCCACCCCAUGCCGAACUGGGUCGUGAAACACAGCAGCGCCAAUGAUACUCGGACCGCAGGGUCCCGGAAAAGUCGGUCAGCGCGGGGGUU |
Experimental Data
Method: X-RAY DIFFRACTION
Deposited Date: 2015-09-08 Deposition Author(s): Connell, S.R. , Fucini, P. , Kaminishi, T. , Ochoa-Lizarralde, B. , Schedlbauer, A.