PDB entry 3cma

View 3cma on RCSB PDB site
Description: The structure of CCA and CCA-Phe-Cap-Bio bound to the large ribosomal subunit of Haloarcula marismortui
Class: ribosome
Keywords: RIBOSOME 50S, PROTEIN-PROTEIN COMPLEX, RNA-RNA COMPLEX, PROTEIN-RNA COMPLEX, PEPTIDYL-tRNA HYDROLYSIS, RIBOSOME
Deposited on 2008-03-21, released 2008-09-23
The last revision prior to the SCOPe 2.05 freeze date was dated 2011-07-13, with a file datestamp of 2011-05-25.
Experiment type: XRAY
Resolution: 2.8 Å
R-factor: 0.194
AEROSPACI score: 0.28 (click here for full SPACI score report)

Chains and heterogens:

  • Chain '0':
    Compound: 23S ribosomal RNA
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
  • Chain '1':
    Compound: 50S ribosomal protein L37e
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d3cma11
  • Chain '2':
    Compound: 50S ribosomal protein L39e
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d3cma21
  • Chain '3':
    Compound: 50S ribosomal protein L44E
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d3cma31
  • Chain '5':
    Compound: RNA (5'-r(*cp*cp*a)-3')
    Species:
    Gene:
  • Chain '6':
    Compound: RNA (5'-r(*cp*cp*(8an))-3')
    Species:
    Gene:
  • Chain '9':
    Compound: 5S ribosomal RNA
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
  • Chain 'A':
    Compound: 50S ribosomal protein L2P
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed):
  • Chain 'B':
    Compound: 50S ribosomal protein L3P
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d3cmab1
  • Chain 'C':
    Compound: 50S ribosomal protein L4P
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed):
  • Chain 'D':
    Compound: 50S ribosomal protein L5P
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d3cmad1
  • Chain 'E':
    Compound: 50S ribosomal protein L6P
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed):
  • Chain 'F':
    Compound: 50S ribosomal protein L7Ae
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d3cmaf1
  • Chain 'G':
    Compound: 50S ribosomal protein L10e
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed):
  • Chain 'H':
    Compound: 50S ribosomal protein L10e
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d3cmah1
  • Chain 'I':
    Compound: 50S ribosomal protein L11P
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d3cmai1
  • Chain 'J':
    Compound: 50S ribosomal protein L13P
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d3cmaj1
  • Chain 'K':
    Compound: 50S ribosomal protein L14P
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d3cmak1
  • Chain 'L':
    Compound: 50S ribosomal protein L15P
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d3cmal1
  • Chain 'M':
    Compound: 50S ribosomal protein L15e
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed):
  • Chain 'N':
    Compound: 50S ribosomal protein L18P
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d3cman1
  • Chain 'O':
    Compound: 50S ribosomal protein L18e
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d3cmao1
  • Chain 'P':
    Compound: 50S ribosomal protein L19e
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d3cmap1
  • Chain 'Q':
    Compound: 50S ribosomal protein L21e
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d3cmaq1
  • Chain 'R':
    Compound: 50S ribosomal protein L22P
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d3cmar1
  • Chain 'S':
    Compound: 50S ribosomal protein L23P
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d3cmas1
  • Chain 'T':
    Compound: 50S ribosomal protein L24P
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d3cmat1
  • Chain 'U':
    Compound: 50S ribosomal protein L24e
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d3cmau1
  • Chain 'V':
    Compound: 50S ribosomal protein L29P
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d3cmav1
  • Chain 'W':
    Compound: 50S ribosomal protein L30P
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d3cmaw1
  • Chain 'X':
    Compound: 50S ribosomal protein L31e
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d3cmax1
  • Chain 'Y':
    Compound: 50S ribosomal protein L32e
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d3cmay1
  • Chain 'Z':
    Compound: 50S ribosomal protein L37Ae
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed):
    • PDB 3CMA
    Domains in SCOPe 2.05: d3cmaz1
  • Heterogens: PHE, MG, NA, SR, CL, K, CD, HOH

PDB Chain Sequences:

  • Chain '0':
    No sequence available.

  • Chain '1':
    Sequence, based on SEQRES records: (download)
    >3cma1 (1:)
    mtgagtpsqgkknttthtkcrrcgeksyhtkkkvcsscgfgksakrrdyewqskage
    

    Sequence, based on observed residues (ATOM records): (download)
    >3cma1 (1:)
    tgagtpsqgkknttthtkcrrcgeksyhtkkkvcsscgfgksakrrdyewqskage
    

  • Chain '2':
    Sequence, based on SEQRES records: (download)
    >3cma2 (2:)
    mgkkskatkkrlakldnqnsrvpawvmlktdrevqrnhkrrhwrrndtde
    

    Sequence, based on observed residues (ATOM records): (download)
    >3cma2 (2:)
    gkkskatkkrlakldnqnsrvpawvmlktdrrnhkrrhwrrndtde
    

  • Chain '3':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3cma3 (3:)
    mqmprrfntycphcnehqehevekvrsgrqtgmkwidrqrernsgigndgkfskvpggdk
    ptkktdlkyrcgecgkahlregwragrlefqe
    

  • Chain '5':
    No sequence available.

  • Chain '6':
    No sequence available.

  • Chain '9':
    No sequence available.

  • Chain 'A':
    No sequence available.

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >3cmaB (B:)
    mpqpsrprkgslgfgprkrstsetprfnswpsddgqpgvqgfagykagmthvvlvndepn
    spregmeetvpvtvietppmravalrayedtpygqrpltevwtdefhseldrtldvpedh
    dpdaaeeqirdaheagdlgdlrlithtvpdavpsvpkkkpdvmetrvgggsvsdrldhal
    divedggehamndifrageyadvagvtkgkgtqgpvkrwgvqkrkgkharqgwrrrignl
    gpwnpsrvrstvpqqgqtgyhqrtelnkrlidigegdeptvdggfvnygevdgpytlvkg
    svpgpdkrlvrfrpavrpndqprldpevryvsnesnqg
    

    Sequence, based on observed residues (ATOM records): (download)
    >3cmaB (B:)
    pqpsrprkgslgfgprkrstsetprfnswpsddgqpgvqgfagykagmthvvlvndepns
    pregmeetvpvtvietppmravalrayedtpygqrpltevwtdefhseldrtldvpedhd
    pdaaeeqirdaheagdlgdlrlithtvpdavpsvpkkkpdvmetrvgggsvsdrldhald
    ivedggehamndifrageyadvagvtkgkgtqgpvkrwgvqkrkgkharqgwrrrignlg
    pwnpsrvrstvpqqgqtgyhqrtelnkrlidigegdeptvdggfvnygevdgpytlvkgs
    vpgpdkrlvrfrpavrpndqprldpevryvsnesnqg
    

  • Chain 'C':
    No sequence available.

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >3cmaD (D:)
    mssesesggdfhemrepriekvvvhmgighggrdlanaedilgeitgqmpvrtkakrtvg
    efdiregdpigakvtlrdemaeeflqtalplaelatsqfddtgnfsfgveehtefpsqey
    dpsigiygldvtvnlvrpgyrvakrdkasrsiptkhrlnpadavafiestydvevse
    

    Sequence, based on observed residues (ATOM records): (download)
    >3cmaD (D:)
    fhemrepriekvvvhmgighanaedilgeitgqmpvrtkakrtvgefdiregdpigakvt
    lrdemaeeflqtalplaelatsqfddtgnfsfgldvtvnlvrpgyrvakrdkasrsiptk
    hrlnpadavafiestydvev
    

  • Chain 'E':
    No sequence available.

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >3cmaF (F:)
    mpvyvdfdvpadleddalealevardtgavkkgtnettksiergsaelvfvaedvqpeei
    vmhipeladekgvpfifveqqddlghaaglevgsaaaavtdageadadvediadkveelr
    

    Sequence, based on observed residues (ATOM records): (download)
    >3cmaF (F:)
    pvyvdfdvpadleddalealevardtgavkkgtnettksiergsaelvfvaedvqpeeiv
    mhipeladekgvpfifveqqddlghaaglevgsaaaavtdageadadvediadkveelr
    

  • Chain 'G':
    No sequence available.

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >3cmaH (H:)
    msdkpasmyrdidkpaytrreyitgipgskiaqhkmgrkqkdaddypvqisliveetvql
    rhgsleasrlsanrhlikelgeegdykmtlrkfphqvlrenkqatgagadrvsdgmraaf
    gkivgtaarvqageqlftaycnvedaehvkeafrraynkitpscrikvergeellia
    

    Sequence, based on observed residues (ATOM records): (download)
    >3cmaH (H:)
    kpasmyrdidkpaytrreyitgipgskiaqhkmgrkqkdaddypvqisliveetvqlrhg
    sleasrlsanrhlikelgeegdykmtlrkfphqvlrenkdgmraafgkivgtaarvqage
    qlftaycnvedaehvkeafrraynkitpscrikvergeel
    

  • Chain 'I':
    Sequence, based on SEQRES records: (download)
    >3cmaI (I:)
    magtievlvpggeanpgpplgpelgptpvdvqavvqeindqtaafdgtevpvtvkydddg
    sfeievgvpptaelikdeagfetgsgepqedfvadlsvdqvkqiaeqkhpdllsydltna
    akevvgtctslgvtiegenprefkeridageyddvfaaeaqa
    

    Sequence, based on observed residues (ATOM records): (download)
    >3cmaI (I:)
    gvpptaelikdeagfetgsgepqedfvadlsvdqvkqiaeqkhpdllsydltnaakevvg
    tctslgvtie
    

  • Chain 'J':
    Sequence, based on SEQRES records: (download)
    >3cmaJ (J:)
    msvaefdadvivdardcimgrvasqvaeqaldgetvavvnaeravitgreeqivekyekr
    vdigndngyfypkrpdgifkrtirgmlphkkqrgreafesvrvylgnpydedgevldgts
    ldrlsnikfvtlgeisetlganktw
    

    Sequence, based on observed residues (ATOM records): (download)
    >3cmaJ (J:)
    aefdadvivdardcimgrvasqvaeqaldgetvavvnaeravitgreeqivekyekrvdi
    gndngyfypkrpdgifkrtirgmlphkkqrgreafesvrvylgnpydedgevldgtsldr
    lsnikfvtlgeisetlganktw
    

  • Chain 'K':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3cmaK (K:)
    mealgadvtqglekgslitcadntgarelkvisvhgysgtknrhpkaglgdkitvsvtkg
    tpemrrqvleavvvrqrkpirrpdgtrvkfednaavivdenedprgtelkgpiarevaqr
    fgsvasaatmiv
    

  • Chain 'L':
    Sequence, based on SEQRES records: (download)
    >3cmaL (L:)
    mtskkkrqrgsrthgggshknrrgaghrggrgdagrdkhefhnheplgksgfkrpqkvqe
    eaatidvreidenvtllaaddvaevedggfrvdvrdvveeaddadyvkvlgagqvrhelt
    liaddfsegarekvegaggsveltdlgeerqaeaeetedadadee
    

    Sequence, based on observed residues (ATOM records): (download)
    >3cmaL (L:)
    tskkkrqrgsrthgggshknrrgaghrggrgdagrdkhefhnheplgksgfkrpqkvqee
    aatidvreidenvtllaaddvaefrvdvrdvveeaddadyvkvlgagqvrheltliaddf
    segarekvegaggsveltdlgeerq
    

  • Chain 'M':
    No sequence available.

  • Chain 'N':
    Sequence, based on SEQRES records: (download)
    >3cmaN (N:)
    matgprykvpmrrrreartdyhqrlrllksgkprlvarksnkhvraqlvtlgpngddtla
    sahssdlaeygweaptgnmpsayltgllaglraqeagveeavldiglnsptpgskvfaiq
    egaidagldiphnddvladwqrtrgahiaeydeqleeplysgdfdaadlpehfdelretl
    ldgdiel
    

    Sequence, based on observed residues (ATOM records): (download)
    >3cmaN (N:)
    atgprykvpmrrrreartdyhqrlrllksgkprlvarksnkhvraqlvtlgpngddtlas
    ahssdlaeygweaptgnmpsayltgllaglraqeagveeavldiglnsptpgskvfaiqe
    gaidagldiphnddvladwqrtrgahiaeydeqleeplysgdfdaadlpehfdelretll
    dgdiel
    

  • Chain 'O':
    Sequence, based on SEQRES records: (download)
    >3cmaO (O:)
    msktnprlssliadlksaarssggavwgdvaerlekprrthaevnlgrieryaqedetvv
    vpgkvlgsgvlqkdvtvaavdfsgtaetkidqvgeavsleqaiennpegshvrvir
    

    Sequence, based on observed residues (ATOM records): (download)
    >3cmaO (O:)
    sktnprlssliadlksaarssggavwgdvaerlekprrthaevnlgrieryaqedetvvv
    pgkvlgsgvlqkdvtvaavdfsgtaetkidqvgeavsleqaiennpegshvrvir
    

  • Chain 'P':
    Sequence, based on SEQRES records: (download)
    >3cmaP (P:)
    mtdlsaqkrlaadvldvgknrvwfnperqgdiadaitredvrelvdegaiqakdkkgnsr
    grarerqkkrayghqkgagsrkgkagarqnskedwesriraqrtklrelrdegtlsssqy
    rdlydkagggefdsvadleryidanhgda
    

    Sequence, based on observed residues (ATOM records): (download)
    >3cmaP (P:)
    tdlsaqkrlaadvldvgknrvwfnperqgdiadaitredvrelvdegaiqakdkkgnsrg
    rarerqkkrayghqkgagsrkgkagarqnskedwesriraqrtklrelrdegtlsssqyr
    dlydkagggefdsvadleryida
    

  • Chain 'Q':
    Sequence, based on SEQRES records: (download)
    >3cmaQ (Q:)
    mpssngplegtrgklknkprdrgtsppqraveefddgekvhlkidpsvpngrfhprfdgq
    tgtvegkqgdaykvdivdggkektiivtaahlrrqe
    

    Sequence, based on observed residues (ATOM records): (download)
    >3cmaQ (Q:)
    pssngplegtrgklknkprdrgtsppqraveefddgekvhlkidpsvpngrfhprfdgqt
    gtvegkqgdaykvdivdggkektiivtaahlrrqe
    

  • Chain 'R':
    Sequence, based on SEQRES records: (download)
    >3cmaR (R:)
    mgisysveadpdttakamlrerqmsfkhskaiareikgktageavdyleaviegdqpvpf
    kqhnsgvghkskvdgwdagrypekaskafldllenavgnadhqgfdgeamtikhvaahkv
    geqqgrkpramgrasawnspqvdvelileepeved
    

    Sequence, based on observed residues (ATOM records): (download)
    >3cmaR (R:)
    gisysveadpdttakamlrerqmsfkhskaiareikgktageavdyleaviegdqpvpfk
    qhnsgvghkskvdgwdagrypekaskafldllenavgnadhqgfdgeamtikhvaahkvg
    eqqgrkpramgrasawnspqvdvelileep
    

  • Chain 'S':
    Sequence, based on SEQRES records: (download)
    >3cmaS (S:)
    mswdvikhphvtekamndmdfqnklqfavddraskgevadaveeqydvtveqvntqntmd
    gekkavvrlsedddaqevasrigvf
    

    Sequence, based on observed residues (ATOM records): (download)
    >3cmaS (S:)
    swdvikhphvtekamndmdfqnklqfavddraskgevadaveeqydvtveqvntqntmdg
    ekkavvrlsedddaqevasri
    

  • Chain 'T':
    Sequence, based on SEQRES records: (download)
    >3cmaT (T:)
    mskqpdkqrksqrraplherhkqvratlsadlreeygqrnvrvnagdtvevlrgdfagee
    gevinvdldkavihvedvtlektdgeevprpldtsnvrvtdldledekrearleseddsa
    

    Sequence, based on observed residues (ATOM records): (download)
    >3cmaT (T:)
    skqpdkqrksqrraplherhkqvratlsadlreeygqrnvrvnagdtvevlrgdfageeg
    evinvdldkavihvedvtlektdgeevprpldtsnvrvtdldledekrearleseddsa
    

  • Chain 'U':
    Sequence, based on SEQRES records: (download)
    >3cmaU (U:)
    mprtrecdycgtdiepgtgtmfvhkdgatthfcsskcennadlgrearnlewtdtargea
    geaedea
    

    Sequence, based on observed residues (ATOM records): (download)
    >3cmaU (U:)
    recdycgtdiepgtgtmfvhkdgatthfcsskcennadlgrearnlewtdtar
    

  • Chain 'V':
    Sequence, based on SEQRES records: (download)
    >3cmaV (V:)
    mtvlhvqeirdmtpaereaelddlktellnaravqaaggapenpgrikelrkaiarikti
    qgeegdlqene
    

    Sequence, based on observed residues (ATOM records): (download)
    >3cmaV (V:)
    tvlhvqeirdmtpaereaelddlktellnaravqaaggapenpgrikelrkaiariktiq
    geegd
    

  • Chain 'W':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3cmaW (W:)
    mhalvqlrgevnmhtdiqdtlemlnihhvnhctlvpetdayrgmvakvndfvafgepsqe
    tletvlatraeplegdadvddewvaehtdyddisglafallseettlreqglsptlrlhp
    prgghdgvkhpvkeggqlgkhdtegiddlleamr
    

  • Chain 'X':
    Sequence, based on SEQRES records: (download)
    >3cmaX (X:)
    msasdfeervvtiplrdaraepnhkradkamilirehlakhfsvdedavrldpsineaaw
    argrantpskirvraarfeeegeaiveaetae
    

    Sequence, based on observed residues (ATOM records): (download)
    >3cmaX (X:)
    ervvtiplrdaraepnhkradkamilirehlakhfsvdedavrldpsineaawargrant
    pskirvraarfeeegeaiveae
    

  • Chain 'Y':
    Sequence, based on SEQRES records: (download)
    >3cmaY (Y:)
    madneedveaeeeyteltdisgvgpskaeslreagfesvedvrgadqsaladvsgignal
    aarikadvggleveseteaeveeeggeeapdedvetelqargltektpdlsdedarlltq
    rhrvgkpqfnrqdhhkkkrvstswrkprgqlskqrrgikgkgdtveagfrsptavrgkhp
    sgfeevrvhnvddlegvdgdteavriaskvgarkrerieeeaedagirvlnptyvevevs
    

    Sequence, based on observed residues (ATOM records): (download)
    >3cmaY (Y:)
    telqargltektpdlsdedarlltqrhrvgkpqfnrqdhhkkkrvstswrkprgqlskqr
    rgikgkgdtveagfrsptavrgkhpsgfeevrvhnvddlegvdgdteavriaskvgarkr
    erieeeaedagirvlnptyvev
    

  • Chain 'Z':
    Sequence, based on SEQRES records: (download)
    >3cmaZ (Z:)
    msprarrepnleglmwplggqqttmasksgktgssgrfgarygrvsrrrvaeiesemned
    hacpncgedrvdrqgtgiwqcsycdykftggsykpetpggktvrrsiraalsedee
    

    Sequence, based on observed residues (ATOM records): (download)
    >3cmaZ (Z:)
    ssgrfgarygrvsrrrvaeiesemnedhacpncgedrvdrqgtgiwqcsycdykftggsy
    kpetpggktvrrs