PDB entry 1yl3

View 1yl3 on RCSB PDB site
Description: Crystal structure of 70S ribosome with thrS operator and tRNAs. Large subunit. The coordinates for the small subunit are in the pdb entry 1YL4.
Class: ribosome
Keywords: ribosome, mRNA, translational operator
Deposited on 2005-01-19, released 2005-04-12
The last revision prior to the SCOPe 2.07 freeze date was dated 2014-12-10, with a file datestamp of 2014-12-05.
Experiment type: XRAY
Resolution: 5.5 Å
R-factor: 0.307
AEROSPACI score: -0.11 (click here for full SPACI score report)

Chains and heterogens:

  • Chain '0':
    Compound: 50S ribosomal protein L17
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d1yl301
  • Chain '1':
    Compound: 50S ribosomal protein L20
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
    • PDB 1YL3 (Start-117)
    Domains in SCOPe 2.07: d1yl311
  • Chain '2':
    Compound: 50S ribosomal protein L21
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
    • PDB 1YL3 (0-99)
    Domains in SCOPe 2.07: d1yl321
  • Chain '3':
    Compound: 50S ribosomal protein L27
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
    • PDB 1YL3
    Domains in SCOPe 2.07: d1yl331
  • Chain '4':
    Compound: 50S ribosomal protein L31
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
    • PDB 1YL3 (0-72)
  • Chain '5':
    Compound: 50S ribosomal protein L32
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
    • PDB 1YL3
    Domains in SCOPe 2.07: d1yl351
  • Chain '6':
    Compound: 50S ribosomal protein L33
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
    • PDB 1YL3
  • Chain '7':
    Compound: 50S ribosomal protein L34
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
    • PDB 1YL3 (0-End)
    Domains in SCOPe 2.07: d1yl371
  • Chain '8':
    Compound: 50S ribosomal protein L35
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
    • PDB 1YL3 (Start-63)
    Domains in SCOPe 2.07: d1yl381
  • Chain '9':
    Compound: 50S ribosomal protein L36
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
    • PDB 1YL3 (Start-35)
    Domains in SCOPe 2.07: d1yl391
  • Chain 'A':
    Compound: 23S ribosomal RNA
    Species: Thermus thermophilus [TaxId:300852]
  • Chain 'B':
    Compound: 5S ribosomal RNA
    Species: Thermus thermophilus [TaxId:300852]
  • Chain 'C':
    Compound: 50s ribosomal protein l1
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d1yl3c1
  • Chain 'D':
    Compound: 50S ribosomal protein L2
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d1yl3d1, d1yl3d2
  • Chain 'E':
    Compound: 50S ribosomal protein L3
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
    • PDB 1YL3
  • Chain 'F':
    Compound: 50S ribosomal protein L4
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
    • PDB 1YL3 (0-245)
    Domains in SCOPe 2.07: d1yl3f1
  • Chain 'G':
    Compound: 50S ribosomal protein L5
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
    • PDB 1YL3
  • Chain 'H':
    Compound: 50S ribosomal protein L6
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
    • PDB 1YL3
    Domains in SCOPe 2.07: d1yl3h1, d1yl3h2
  • Chain 'I':
    Compound: 50S ribosomal protein L7/L12
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
    • PDB 1YL3 (0-127)
    Domains in SCOPe 2.07: d1yl3i1, d1yl3i2
  • Chain 'J':
    Compound: 50S ribosomal protein L7/L12
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
    • PDB 1YL3 (0-127)
    Domains in SCOPe 2.07: d1yl3j1, d1yl3j2
  • Chain 'K':
    Compound: 50S ribosomal protein L9
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
    • PDB 1YL3 (0-148)
    Domains in SCOPe 2.07: d1yl3k1, d1yl3k2
  • Chain 'L':
    Compound: 50S ribosomal protein L11
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
    • PDB 1YL3
    Domains in SCOPe 2.07: d1yl3l1, d1yl3l2
  • Chain 'M':
    Compound: 50S ribosomal protein L13
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
    • PDB 1YL3
    Domains in SCOPe 2.07: d1yl3m1
  • Chain 'N':
    Compound: 50S ribosomal protein L14
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
    • PDB 1YL3 (0-121)
    Domains in SCOPe 2.07: d1yl3n1
  • Chain 'O':
    Compound: 50S ribosomal protein L15
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
    • PDB 1YL3
  • Chain 'P':
    Compound: 50S ribosomal protein L16
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
    • PDB 1YL3 (0-137)
  • Chain 'Q':
    Compound: 50S ribosomal protein L18
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
    • PDB 1YL3
  • Chain 'R':
    Compound: 50S ribosomal protein L19
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
    • PDB 1YL3
    Domains in SCOPe 2.07: d1yl3r1
  • Chain 'S':
    Compound: 50S ribosomal protein L22
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d1yl3s1
  • Chain 'T':
    Compound: 50S ribosomal protein L23
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
    • PDB 1YL3 (0-End)
    Domains in SCOPe 2.07: d1yl3t1
  • Chain 'U':
    Compound: 50S ribosomal protein L24
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
    • PDB 1YL3 (0-End)
    Domains in SCOPe 2.07: d1yl3u1
  • Chain 'V':
    Compound: 50S general stress protein CTC (L25)
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
    • PDB 1YL3
    Domains in SCOPe 2.07: d1yl3v1
  • Chain 'W':
    Compound: 50S ribosomal protein L29
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
    • PDB 1YL3 (0-End)
    Domains in SCOPe 2.07: d1yl3w1
  • Chain 'X':
    Compound: 50S ribosomal protein L30
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d1yl3x1

PDB Chain Sequences:

  • Chain '0':
    Sequence, based on SEQRES records: (download)
    >1yl30 (0:)
    mrhlksgrklnrhsshrlalyrnqaksllthgritttvpkakelrgfvdhlihlakrgdl
    harrlvlrdlqdvklvrklfdeiapryrdrqggytrvlklaerrrgdgaplalvelve
    

    Sequence, based on observed residues (ATOM records): (download)
    >1yl30 (0:)
    sshrlalyrnqaksllthgritttvpkakelrgfvdhlihlakrgdlharrlvlrdlqdv
    klvrklfdeiapryrdrqggytrvlklaerrrgdgaplalvelve
    

  • Chain '1':
    Sequence, based on SEQRES records: (download)
    >1yl31 (1:)
    mpraktgivrrrrhkkvlkrakgfwgsrskqyrnafqtllnaatyeyrdrrnkkrdfrrl
    wiqrinagarlhgmnystfinglkranidlnrkvladiaarepeafkalvdasrnarq
    

    Sequence, based on observed residues (ATOM records): (download)
    >1yl31 (1:)
    praktgivrrrrhkkvlkrakgfwgsrskqyrnafqtllnaatyeyrdrrnkkrdfrrlw
    iqrinagarlhgmnystfinglkranidlnrkvladiaarepeafkalvdasrnarq
    

  • Chain '2':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1yl32 (2:)
    mfaiiqtggkqyrvsegdvirveslqgeagdkvelkalfvggeqtvfgedagkytvqaev
    vehgrgkkiyirkyksgvqyrrrtghrqnftaikilgiqg
    

  • Chain '3':
    Sequence, based on SEQRES records: (download)
    >1yl33 (3:)
    mahkkgvgsskngrdsnpkylgvkkfggevvkagnilvrqrgtkfkagqgvgmgrdhtlf
    alsdgkvvfinkgkgarfisieaaqtevaad
    

    Sequence, based on observed residues (ATOM records): (download)
    >1yl33 (3:)
    ahkkgvgsskngrdsnpkylgvkkfggevvkagnilvrqrgtkfkagqgvgmgrdhtlfa
    lsdgkvvfinkgkgarfisieaaqte
    

  • Chain '4':
    No sequence available.

  • Chain '5':
    Sequence, based on SEQRES records: (download)
    >1yl35 (5:)
    makhpvpkkktskskrdmrrshhaltapnltecpqchgkklshhicpncgyydgrqvlav
    

    Sequence, based on observed residues (ATOM records): (download)
    >1yl35 (5:)
    akhpvpkkktskskrdmrrshhaltapnltecpqchgkklshhicpncgyydgrqvla
    

  • Chain '6':
    No sequence available.

  • Chain '7':
    Sequence, based on SEQRES records: (download)
    >1yl37 (7:)
    mkrtyqpnnrkrakthgfrarmktksgrnilarrrakgrhqltvsde
    

    Sequence, based on observed residues (ATOM records): (download)
    >1yl37 (7:)
    mkrtyqpnnrkrakthgfrarmktksgrnilarrrakgrhqltvsd
    

  • Chain '8':
    Sequence, based on SEQRES records: (download)
    >1yl38 (8:)
    mpkmkthkmakrrikitgtgkvmafksgkrhqntgksgdeirgkgkgfvlakaewarmkl
    mlpr
    

    Sequence, based on observed residues (ATOM records): (download)
    >1yl38 (8:)
    pkmkthkmakrrikitgtgkvmafksgkrhqntgksgdeirgkgkgfvlakaewarmklm
    lpr
    

  • Chain '9':
    Sequence, based on SEQRES records: (download)
    >1yl39 (9:)
    mkvrssvkkmcdnckvvrrhgrvlvicsnvkhkqrq
    

    Sequence, based on observed residues (ATOM records): (download)
    >1yl39 (9:)
    kvrssvkkmcdnckvvrrhgrvlvicsnvkhkqrq
    

  • Chain 'A':
    No sequence available.

  • Chain 'B':
    No sequence available.

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >1yl3C (C:)
    pkhgkryrallekvdpnkiytideaahlvkelatakfdetvevhaklgidprrsdqnvrg
    tvslphglgkqvrvlaiakgekikeaeeagadyvggeeiiqkildgwmdfdavvatpdvm
    gavgsklgrilgprgllpnpkagtvgfnigeiireikagriefrndktgaihapvgkasf
    ppekladnirafiraleahkpegakgtflrsvyvtttmgpsvrinphs
    

    Sequence, based on observed residues (ATOM records): (download)
    >1yl3C (C:)
    kryrallekvdpnkiytideaahlvkelatakfdetvevhaklgidprrsdqnvrgtvsg
    lgkqvrvlaiakgekikeaeeagadyvggeeiiqkildgwmdfdavvatpdvmgavgskl
    grilgprgllpnpkagtvgfnigeiireikagriefrndktgaihapvgkasfppeklad
    nirafiraleahkpegakgtflrsvyvtttmgpsvrinphs
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >1yl3D (D:)
    qyriidfkrdkdgipgrvatieydpnrsanialinyadgekryiiapknlkvgmeimsgp
    dadikignalplenipvgtlvhnielkpgrggqlvraagtsaqvlgkegkyvivrlasge
    vrmilgkcratvgevgnggrtdkpfvkagnkhhkmkargtkwpnvrgvamnavdhpfg
    

    Sequence, based on observed residues (ATOM records): (download)
    >1yl3D (D:)
    qyriidfkrdkdgipgrvatieydpnrsanialinyadgekryiiapknlkvgmeimsgp
    dadikignalplenipvgtlvhnielkpgrggqlvraagtsaqvlgkegkyvivrlasge
    vrmilgkcratvgevgnggrtdkpfvkagnkhhkmkapnvrgvamnavdhpfg
    

  • Chain 'E':
    No sequence available.

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >1yl3F (F:)
    meatiydldgntdgevdlpdvfetpvrsdligkavraaqanrkqdygsdeyaglrtpaes
    fgsgrgqahvpkldgrarrvpqavkgrsahppktekdrsldlndkerqlavrsalaatad
    adlvadrghefdrdevpvvvsddfedlvktqevvsllealdvhadidradetkikagqgs
    argrkyrrpasilfvtsdepstaarnlagadvatasevntedlapggapgrltvftesal
    aevaer
    

    Sequence, based on observed residues (ATOM records): (download)
    >1yl3F (F:)
    meatiydntdgevdlpdvfetpvrsdligkavraaqanrkqdygsdeyaglrtpaesfgs
    grgqahrvpqavkgrsahppktekdrsldlndkerqlavrsalaatadvvvsddfedlvk
    tqevvsllealdvhadidrlfvtsdepstaarnlagadvatasevntedlapgrltvfte
    salaevaer
    

  • Chain 'G':
    No sequence available.

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >1yl3H (H:)
    srvgkkpieipagvtvtvngntvtvkgpkgeltrtfhpdmtitvegnvitvtrpsdekhh
    ralhgttrsllanmvegvskgyekalelvgvgyraskqgkklvlsvgyshpveiepeegl
    eievpsqtkiivkgadkqrvgelaaniravrppepykgkgiryegelvrlkegktgk
    

    Sequence, based on observed residues (ATOM records): (download)
    >1yl3H (H:)
    pieipagvtvtvngntvtvkgpkgeltrtfhpdmtitvegnvitvtrpsdekhhralhgt
    trsllanmvegvskgyekalelvgvgyraskqgkklvlsvgyshpveiepeegleievps
    qtkiivkgadkqrvgelaaniravrppepykgkgiryegelvrl
    

  • Chain 'I':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1yl3I (I:)
    mtideiieaiekltvselaelvkkledkfgvtaaapvavaaapvagaaagaaqeektefd
    vvlksfgqnkiqvikvvreitglglkeakdlvekagspdaviksgvskeeaeeikkklee
    agaevelk
    

  • Chain 'J':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1yl3J (J:)
    mtideiieaiekltvselaelvkkledkfgvtaaapvavaaapvagaaagaaqeektefd
    vvlksfgqnkiqvikvvreitglglkeakdlvekagspdaviksgvskeeaeeikkklee
    agaevelk
    

  • Chain 'K':
    Sequence, based on SEQRES records: (download)
    >1yl3K (K:)
    mkviflkdvkgkgkkgeiknvadgyannflfkqglaieatpanlkaleaqkqkeqrqaae
    elanakklkeqlekltvtipakageggrlfgsitskqiaeslqaqhglkldkrkielada
    iralgytnvpvklhpevtatlkvhvteqk
    

    Sequence, based on observed residues (ATOM records): (download)
    >1yl3K (K:)
    mkviflkdvkgkgkkgeiknvadgyannflfkqglaieatpanlkaleaqkqkeqrqaae
    elanakklkeqlekltvtipakagegrlfgsitskqiaeslqaqhglkldkrkieladai
    ralgytnvpvklhpevtatlkvhvteqk
    

  • Chain 'L':
    Sequence, based on SEQRES records: (download)
    >1yl3L (L:)
    makkvaaqiklqlpagkatpappvgpalgqhgvnimefckrfnaetadkagmilpvvitv
    yedksftfiiktppasfllkkaagiekgssepkrkivgkvtrkqieeiaktkmpdlnans
    leaamkiiegtaksmgievvd
    

    Sequence, based on observed residues (ATOM records): (download)
    >1yl3L (L:)
    qiklqlpagkatpappvgpalgqhgvnimefckrfnaetadkagmilpvvitvyedksft
    fiiktppasfllkkaagiekgssepkrkivgkvtrkqieeiaktkmpdlnansleaamki
    iegtaksmgievv
    

  • Chain 'M':
    Sequence, based on SEQRES records: (download)
    >1yl3M (M:)
    msvaefdadvivdardcimgrvasqvaeqaldgetvavvnaeravitgreeqivekyekr
    vdigndngyfypkrpdgifkrtirgmlphkkqrgreafesvrvylgnpydedgevldgts
    ldrlsnikfvtlgeisetlganktw
    

    Sequence, based on observed residues (ATOM records): (download)
    >1yl3M (M:)
    aefdadvivdardcimgrvasqvaeqaldgetvavvnaeravitgreeqivekyekrvdi
    gndngyfypkrpdgifkrtirgmlpkkqrgreafesvrvylgnpydtlgeisetlga
    

  • Chain 'N':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1yl3N (N:)
    miqqesrlkvadnsgarevlvikvlggsgrryanigdvvvatvkdatpggvvkkgqvvka
    vvvrtkrgvrrpdgsyirfdenacviirddksprgtrifgpvarelrdkdfmkiislape
    vi
    

  • Chain 'O':
    No sequence available.

  • Chain 'P':
    No sequence available.

  • Chain 'Q':
    No sequence available.

  • Chain 'R':
    Sequence, based on SEQRES records: (download)
    >1yl3R (R:)
    prtrecdycgtdiepgtgtmfvhkdgatthfcsskcennadlgrearnlewtdtargeag
    eaedea
    

    Sequence, based on observed residues (ATOM records): (download)
    >1yl3R (R:)
    recdycgtdiepgtgtmfvhkdgatthfcsskcennadlrearnlewtdtar
    

  • Chain 'S':
    Sequence, based on SEQRES records: (download)
    >1yl3S (S:)
    meakaiaryvrisprkvrlvvdlirgksleearnilrytnkrgayfvakvlesaaanavn
    nhdmledrlyvkaayvdegpalkrvlprargradiikkrtshitvilgekhgk
    

    Sequence, based on observed residues (ATOM records): (download)
    >1yl3S (S:)
    eakaiaryvrisprkvrlvvdlirgksleearnilrytnkrgayfvakvlesaaanavnn
    hdledrlyvkaayvdegpalkrvlprargradiikkrtshitvilgek
    

  • Chain 'T':
    Sequence, based on SEQRES records: (download)
    >1yl3T (T:)
    swdvikhphvtekamndmdfqnklqfavddraskgevadaveeqydvtveqvntqntmdg
    ekkavvrlsedddaqevasrigvf
    

    Sequence, based on observed residues (ATOM records): (download)
    >1yl3T (T:)
    swdvikhphvtekamndmdfnklqfavddraskgevadaveeqydvtveqvntqntmdge
    kkavvrlsedddqeva
    

  • Chain 'U':
    Sequence, based on SEQRES records: (download)
    >1yl3U (U:)
    skqpdkqrksqrraplherhkqvratlsadlreeygqrnvrvnagdtvevlrgdfageeg
    evinvdldkavihvedvtlektdgeevprpldtsnvrvtdldledekrearleseddsa
    

    Sequence, based on observed residues (ATOM records): (download)
    >1yl3U (U:)
    skqpdkqrksqrraplherhkqvratlsadlreeygvrvnagdtvevlrgdfageegevi
    nvdldkavihvedvtlektdgeevprpldtsnvrvtdldledekrearle
    

  • Chain 'V':
    Sequence, based on SEQRES records: (download)
    >1yl3V (V:)
    mahtgqtaksqgdtatmeltakprtpkqkldesmiaavaynkennvsfaldrkafdrafr
    qqsttglfditveggetfpalvkavqmdkrkrapihvdfymvtygepvevsvpvhttgrs
    qgevqgglvdivvhnlqivapgprripqelvvdvtkmnigdhitagdiklpegctlaadp
    eltvvsvlpprltaeeleaevqaaqvaglvaagelseeaaeavlegdasleevkaeased
    nagtdsednsdaq
    

    Sequence, based on observed residues (ATOM records): (download)
    >1yl3V (V:)
    meltakprtpkqkldesmiaavaynkennvsfaldrkafdrafrqqsttglfditvegge
    tfpalvkavqmdkrkrapihvdfymvtygepvevsvpvhttgrsqgevqgglvdivvhnl
    qivapgprripqelvvdvtkmnigdhitagdiklpegctlaadpeltvvsvlpprlt
    

  • Chain 'W':
    Sequence, based on SEQRES records: (download)
    >1yl3W (W:)
    tvlhvqeirdmtpaereaelddlktellnaravqaaggapenpgrikelrkaiariktiq
    geegdlqene
    

    Sequence, based on observed residues (ATOM records): (download)
    >1yl3W (W:)
    tvlhvqeirdmtpaereaelddlktellnarvqaaggapenpgrikelrkaiariktiqg
    eegd
    

  • Chain 'X':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1yl3X (X:)
    mprlkvklvkspigypkdqkaalkalglrrlqqervledtpairgnvekvahlvrvevve