PDB entry 3dll

View 3dll on RCSB PDB site
Description: The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning
Class: ribosome
Keywords: Ribosome, Antibiotic, oxazolidinone, Linezolid, Ribonucleoprotein, Ribosomal protein, RNA-binding, rRNA-binding, tRNA-binding, Methylation, Metal-binding, Zinc-finger
Deposited on 2008-06-27, released 2008-09-16
The last revision prior to the SCOPe 2.06 freeze date was dated 2015-07-22, with a file datestamp of 2015-07-17.
Experiment type: XRAY
Resolution: 3.5 Å
R-factor: N/A
AEROSPACI score: 0.05 (click here for full SPACI score report)

Chains and heterogens:

  • Chain '1':
    Compound: 50S ribosomal protein L33
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3dll11
  • Chain '2':
    Compound: 50S ribosomal protein L34
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3dll21
  • Chain '3':
    Compound: 50S ribosomal protein L35
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3dll31
  • Chain '4':
    Compound: 50S ribosomal protein L36
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3dll41
  • Chain 'A':
    Compound: 50S ribosomal protein L2
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed):
  • Chain 'B':
    Compound: 50S ribosomal protein L3
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3dllb1
  • Chain 'C':
    Compound: 50S ribosomal protein L4
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3dllc1
  • Chain 'D':
    Compound: 50S ribosomal protein L5
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3dlld1
  • Chain 'E':
    Compound: 50S ribosomal protein L6
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3dlle1, d3dlle2
  • Chain 'F':
    Compound: 50S ribosomal protein L11
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed):
  • Chain 'G':
    Compound: 50S ribosomal protein L13
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3dllg1
  • Chain 'H':
    Compound: 50S ribosomal protein L14
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3dllh1
  • Chain 'I':
    Compound: 50S ribosomal protein L15
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3dlli1
  • Chain 'J':
    Compound: 50S ribosomal protein L16
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3dllj1
  • Chain 'K':
    Compound: 50S ribosomal protein L17
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3dllk1
  • Chain 'L':
    Compound: 50S ribosomal protein L18
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3dlll1
  • Chain 'M':
    Compound: 50S ribosomal protein L19
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3dllm1
  • Chain 'N':
    Compound: 50S ribosomal protein L20
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3dlln1
  • Chain 'O':
    Compound: 50S ribosomal protein L21
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3dllo1
  • Chain 'P':
    Compound: 50S ribosomal protein L22
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3dllp1
  • Chain 'Q':
    Compound: 50S ribosomal protein L23
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3dllq1
  • Chain 'R':
    Compound: 50S ribosomal protein L24
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3dllr1
  • Chain 'S':
    Compound: 50S ribosomal protein L25
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3dlls1
  • Chain 'T':
    Compound: 50S ribosomal protein L27
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3dllt1
  • Chain 'U':
    Compound: 50S ribosomal protein L28
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3dllu1
  • Chain 'V':
    Compound: 50S ribosomal protein L29
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3dllv1
  • Chain 'W':
    Compound: 50S ribosomal protein L30
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3dllw1
  • Chain 'X':
    Compound: rRNA-23S ribosomal RNA
    Species: Deinococcus radiodurans [TaxId:1299]
  • Chain 'Y':
    Compound: 50S ribosomal protein L32
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3dlly1
  • Chain 'Z':
    Compound: rRNA-5S ribosomal RNA
    Species: Deinococcus radiodurans [TaxId:1299]
  • Heterogens: ZN, MG, ZLD

PDB Chain Sequences:

  • Chain '1':
    Sequence, based on SEQRES records: (download)
    >3dll1 (1:)
    makdgpriivkmessagtgfyytttknrrntqaklelkkydpvakkhvvfrekkv
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dll1 (1:)
    akdgpriivkmessagtgfyytttknrrntqaklelkkydpvakkhvvfrekk
    

  • Chain '2':
    Sequence, based on SEQRES records: (download)
    >3dll2 (2:)
    mkrtyqpnnrkrakthgfrarmktksgrnilarrrakgrhqltvsde
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dll2 (2:)
    mkrtyqpnnrkrakthgfrarmktksgrnilarrrakgrhqltvsd
    

  • Chain '3':
    Sequence, based on SEQRES records: (download)
    >3dll3 (3:)
    mpkmkthkmakrrikitgtgkvmafksgkrhqntgksgdeirgkgkgfvlakaewarmkl
    mlprgk
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dll3 (3:)
    pkmkthkmakrrikitgtgkvmafksgkrhqntgksgdeirgkgkgfvlakaewarmklm
    lpr
    

  • Chain '4':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3dll4 (4:)
    mkvrssvkkmcdnckvvrrhgrvlvicsnvkhkqrqg
    

  • Chain 'A':
    No sequence available.

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >3dllB (B:)
    mkgilgtkigmtqiwkndraipvtvvlagpcpivqrktaqtdgyeavqigyapkaerkvn
    kpmqghfakagvaptrilrefrgfapdgdsvnvdifaegekidatgtskgkgtqgvmkrw
    nfaggpashgskkwhrrpgsigqrktpgrvykgkrmaghmgmervtvqnlevveiragen
    lilvkgaipgangglvvlrsaakasaakggk
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dllB (B:)
    mkgilgtkigmtqiwkndraipvtvvlagpcpivqrktaqtdgyeavqigyapkaerkvn
    kpmqghfakagvaptrilrefrgfapdgdsvnvdifaegekidatgtskgkgtqgvmkrw
    nfaggpashgskkwhrrpgsigqrktpgrvykgkrmaghmgmervtvqnlevveiragen
    lilvkgaipgangglvvlrsaakas
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >3dllC (C:)
    maqinvigqnggrtielplpevnsgvlhevvtwqlasrrrgtastrtraqvsktgrkmyg
    qkgtgnarhgdrsvptfvgggvafgpkprsydytlprqvrqlglamaiasrqeggklvav
    dgfdiadaktknfiswakqngldgtekvllvtddentrraarnvswvsvlpvagvnvydi
    lrhdrlvidaaaleiveeeageeqq
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dllC (C:)
    aqinvigqnggrtielplpevnsgvlhevvtwqlasrrrgtastrtraqvsktgrkmygq
    kgtgnarhgdrsvptfvgggvafgpkprsydytlprqvrqlglamaiasrqeggklvavd
    gfdiadaktknfiswakqngldgtekvllvtddentrraarnvswvsvlpvagvnvydil
    rhdrlvidaaaleivee
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >3dllD (D:)
    mqqlktkyndqvrpalmqqfgyssvmavpriekivvneglgsskedskaidkaakelali
    tlqkpiitkakksisnfklrqgmpvgikvtlrgermyvflekliniglprirdfrginpn
    afdgrgnynlgikeqlifpeitydmvdktrgmditivttaktdeearallqsmglpfrkq
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dllD (D:)
    qlktkyndqvrpalmqqfgyssvmavpriekivvneglgsskedskaidkaakelalitl
    qkpiitkakksisnfklrqgmpvgikvtlrgermyvflekliniglprirdfrginpnaf
    dgrgnynlgikeqlifpeitydmvdktrgmditivttaktdeearallqsmglpfrk
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >3dllE (E:)
    msrigkqpiavpsgvtvnaqdgvfkvkgpkgeltvpynteltvrqdgdqllverpsdaqk
    hralhgltrtlvanavkgvsdgytinlelrgvgfrakltgkalemnigyshpviieppag
    vtfavpeptridvsgidkqlvgqvaanvrkvrkpdayhgkgvrfvgeqialkagkagatg
    gkgkk
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dllE (E:)
    gkqpiavpsgvtvnaqdgvfkvkgpkgeltvpynteltvrqdgdqllverpsdaqkhral
    hgltrtlvanavkgvsdgytinlelrgvgfrakltgkalemnigyshpviieppagvtfa
    vpeptridvsgidkqlvgqvaanvrkvrkpdayhgkgvrfvgeqialkagk
    

  • Chain 'F':
    No sequence available.

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >3dllG (G:)
    mafpdtdvspprggpsspakspllrsfkvktyipkndeqnwvvvdasgvplgrlatlias
    rirgkhrpdftpnmiqgdfvvvinaaqvaltgkklddkvytrytgyqgglktetareals
    khperviehavfgmlpkgrqgramhtrlkvyagethphsaqkpqvlktqplevk
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dllG (G:)
    ktyipkndeqnwvvvdasgvplgrlatliasrirgkhrpdftpnmiqgdfvvvinaaqva
    ltgkklddkvytrytgyqgglktetarealskhperviehavfgmlpkgrqgramhtrlk
    vyagethphsaqkpqvlktqpl
    

  • Chain 'H':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3dllH (H:)
    mimpqsrldvadnsgareimcirvlnsgiggkglttggggnkryahvgdiivasvkdaap
    rgavkagdvvkavvvrtshaikradgstirfdrnaaviinnqgeprgtrvfgpvarelrd
    rrfmkivslapevl
    

  • Chain 'I':
    Sequence, based on SEQRES records: (download)
    >3dllI (I:)
    mklhdlkptpgsrkdrkrvgrgpggtdktagrghkgqksrsgagkgaffeggrsrliarl
    pkrgfnnvgttyevvklsqlqdledttfdrdtleayrlvrrknrpvkllasgeisravtv
    hvdaasaaaikaveaaggrvvlpevqtqqddaqkae
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dllI (I:)
    hdlkptpgsrkdrkrvgrgpggtdktagrghkgqksrsgagkgaffeggrsrliarlpkr
    gfnnvgttyevvklsqlqdledttfdrdtleayrlvrrknrpvkllasgeisravtvhvd
    aasaaaikaveaaggrvvlpe
    

  • Chain 'J':
    Sequence, based on SEQRES records: (download)
    >3dllJ (J:)
    mmllpkrtkfrkqfrgrmtgdakggdyvafgdygliamepawiksnqieacrivmsrhfr
    rggkiyirifpdkpvtkkpaetrmgkgkgaveywvsvvkpgrvmfevagvteeqakeafr
    laghklpiqtkmvkrevydeaq
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dllJ (J:)
    krtkfrkqfrgrmtgdakggdyvafgdygliamepawiksnqieacrivmsrhfrrggki
    yirifpdkpvtkkpaetrmgkgkgaveywvsvvkpgrvmfevagvteeqakeafrlaghk
    lpiqtkmvkrevydea
    

  • Chain 'K':
    Sequence, based on SEQRES records: (download)
    >3dllK (K:)
    mrhgkagrklnrnssarvalaraqatallregriqttltkakelrpfveqlittakggdl
    hsrrlvaqdihdkdvvrkvmdevapkyaerpggytrilrvgtrrgdgvtmalielv
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dllK (K:)
    hgkagrklnrnssarvalaraqatallregriqttltkakelrpfveqlittakggdlhs
    rrlvaqdihdkdvvrkvmdevapkyaerpggytrilrvgtrrgdgvtmaliel
    

  • Chain 'L':
    Sequence, based on SEQRES records: (download)
    >3dllL (L:)
    matattirrklrtrrkvrtttaasgrlrlsvyrsskhiyaqiiddsrgqtlaaassaalk
    sgnktdtaaavgkalaaaaaekgikqvvfdrgsykyhgrvkaladaareggldf
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dllL (L:)
    rrklrtrrkvrtttaasgrlrlsvyrsskhiyaqiiddsrgqtlaaassaalksgnktdt
    aaavgkalaaaaaekgikqvvfdrgsykyhgrvkaladaaregg
    

  • Chain 'M':
    Sequence, based on SEQRES records: (download)
    >3dllM (M:)
    mqthikinrgellrgieqdhtrqlpdfrpgdtvrvdtkvregnrtrsqafegvviaings
    gsrksftvrkisfgegvervfpfasplvnqvtivergkvrraklyylrelrgkaariksd
    rsrvmkdaaraqqdkanasasqaaaaqadvtvisaapevapetqge
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dllM (M:)
    qthikinrgellrgieqdhtrqlpdfrpgdtvrvdtkvregnrtrsqafegvviaingsg
    srksftvrkisfgegvervfpfasplvnqvtivergkvrraklyylre
    

  • Chain 'N':
    Sequence, based on SEQRES records: (download)
    >3dllN (N:)
    mpraktgivrrrrhkkvlkrakgfwgsrskqyrnafqtllnaatyeyrdrrnkkrdfrrl
    wiqrinagarlhgmnystfinglkranidlnrkvladiaarepeafkalvdasrnarq
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dllN (N:)
    praktgivrrrrhkkvlkrakgfwgsrskqyrnafqtllnaatyeyrdrrnkkrdfrrlw
    iqrinagarlhgmnystfinglkranidlnrkvladiaarepeafkalvdasrnarq
    

  • Chain 'O':
    Sequence, based on SEQRES records: (download)
    >3dllO (O:)
    mfaiiqtggkqyrvsegdvirveslqgeagdkvelkalfvggeqtvfgedagkytvqaev
    vehgrgkkiyirkyksgvqyrrrtghrqnftaikilgiqg
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dllO (O:)
    iqtggkqyrvsegdvirveslqgeagdkvelkalfvggeqtvfgedagkytvqaevvehg
    rgkkiyirkyksgvqyrrrtghrqnftaikilgi
    

  • Chain 'P':
    Sequence, based on SEQRES records: (download)
    >3dllP (P:)
    mtapeqtfrnkkqrkqqvklrkpgfavakyvrmsprkvrlvvdvirgksvqdaedllrfi
    prsasepvakvlnsakanalhndemledrlfvkeayvdagptlkrliprargsaniikkr
    tshitiivaekgnk
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dllP (P:)
    frnkkqrkqqvklrkpgfavakyvrmsprkvrlvvdvirgksvqdaedllrfiprsasep
    vakvlnsakanalhndemledrlfvkeayvdagptlkrliprargsaniikkrtshitii
    vaekgnk
    

  • Chain 'Q':
    Sequence, based on SEQRES records: (download)
    >3dllQ (Q:)
    mshydilqapvisekaysamergvysfwvspkatkteikdaiqqafgvrvigistmnvpg
    krkrvgrfigqrndrkkaivrlaegqsiealagqa
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dllQ (Q:)
    shydilqapvisekaysamergvysfwvspkatkteikdaiqqafgvrvigistmnvpgk
    rkrvgrfigqrndrkkaivrlaegqsiealagq
    

  • Chain 'R':
    Sequence, based on SEQRES records: (download)
    >3dllR (R:)
    mprpsagshhndklhfkkgdtvivlsgkhkgqtgkvllalprdqkvvvegvnvitknvkp
    smtnpqggqeqrelalhaskvalvdpetgkatrvrkqivdgkkvrvavasgktid
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dllR (R:)
    psagshhndklhfkkgdtvivlsgkhkgqtgkvllalprdqkvvvegvnvitknvkpsmt
    npqggqeqrelalhaskvalvdpetgkatrvrkqivdgkkvrvavasgkt
    

  • Chain 'S':
    Sequence, based on SEQRES records: (download)
    >3dllS (S:)
    meltakprtpkqkldesmiaavaynkennvsfaldrkafdrafrqqsttglfditvegge
    tfpalvkavqmdkrkrapihvdfymvtygepvevsvpvhttgrsqgevqgglvdivvhnl
    qivapgprripqelvvdvtkmnigdhitagdiklpegctlaadpeltvvsvlpprltaee
    leaevqaaqvaglvaagelseeaaeavlegdasleevkaeasednagtdsednsdaq
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dllS (S:)
    meltakprtpkqkldesmiaavaynkennvsfaldrkafdrafrqqsttglfditvegge
    tfpalvkavqmdkrkrapihvdfymvtygepvevsvpvhttgrsqgevqgglvdivvhnl
    qivapgprripqelvvdvtkmnigdhitagdiklpegctlaadpeltvvsvlppr
    

  • Chain 'T':
    Sequence, based on SEQRES records: (download)
    >3dllT (T:)
    mahkkgvgsskngrdsnpkylgvkkfggevvkagnilvrqrgtkfkagqgvgmgrdhtlf
    alsdgkvvfinkgkgarfisieaaqtevaad
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dllT (T:)
    ahkkgvgsskngrdsnpkylgvkkfggevvkagnilvrqrgtkfkagqgvgmgrdhtlfa
    lsdgkvvfinkgkgarfisieaaq
    

  • Chain 'U':
    Sequence, based on SEQRES records: (download)
    >3dllU (U:)
    msrecyltgkknlvvnsvirrgkaradggvgrkttgitkrvqranlhkkairengqvktv
    wlsanalrtlskgpykgieli
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dllU (U:)
    tgkknlvvnsvirrgkaradggvgrkttgitkrvqranlhkkairengqvktvwlsanal
    rtlskgpykgie
    

  • Chain 'V':
    Sequence, based on SEQRES records: (download)
    >3dllV (V:)
    mkpsemrnlqatdfakeidarkkelmelrfqaaagqlaqphrvrqlrrevaqlntvkael
    arkgeqq
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dllV (V:)
    mkpsemrnlqatdfakeidarkkelmelrfqaaagqlaqphrvrqlrrevaqlntvkael
    arkgeq
    

  • Chain 'W':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3dllW (W:)
    mkiklvrsvigrpgnqvktvqalglrkigdsrevsdtpavrgmvktvkhllevqe
    

  • Chain 'X':
    No sequence available.

  • Chain 'Y':
    Sequence, based on SEQRES records: (download)
    >3dllY (Y:)
    makhpvpkkktskskrdmrrshhaltapnltecpqchgkklshhicpncgyydgrqvlav
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dllY (Y:)
    akhpvpkkktskskrdmrrshhaltapnltecpqchgkklshhicpncgyydgrqvla
    

  • Chain 'Z':
    No sequence available.