PDB entry 1n8r

View 1n8r on RCSB PDB site
Description: Structure of large ribosomal subunit in complex with virginiamycin M
Class: ribosome
Keywords: ribosome, virginiamycin M, streptogramin, antibiotic
Deposited on 2002-11-21, released 2003-07-22
The last revision prior to the SCOPe 2.01 freeze date was dated 2009-02-24, with a file datestamp of 2009-03-01.
Experiment type: XRAY
Resolution: 3 Å
R-factor: 0.201
AEROSPACI score: 0.24 (click here for full SPACI score report)

Chains and heterogens:

  • Chain '1':
    Compound: 50S ribosomal protein L37Ae
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed):
    • PDB 1N8R (0-72)
    Domains in SCOPe 2.01: d1n8r1_
  • Chain '2':
    Compound: 50S ribosomal protein L37e
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d1n8r2_
  • Chain '3':
    Compound: 50S ribosomal protein L39e
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d1n8r3_
  • Chain '4':
    Compound: 50S ribosomal protein L44E
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d1n8r4_
  • Chain 'A':
    Compound: 23S ribosomal RNA
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
  • Chain 'B':
    Compound: 5S ribosomal RNA
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
  • Chain 'C':
    Compound: 50S ribosomal protein L2P
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d1n8rc1, d1n8rc2
  • Chain 'D':
    Compound: 50S ribosomal protein L3P
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed):
    • Uniprot P20279 (0-336)
      • conflict (309)
    Domains in SCOPe 2.01: d1n8rd_
  • Chain 'E':
    Compound: 50S ribosomal protein L4E
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d1n8re_
  • Chain 'F':
    Compound: 50S ribosomal protein L5P
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d1n8rf_
  • Chain 'G':
    Compound: 50S ribosomal protein L6P
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d1n8rg1, d1n8rg2
  • Chain 'H':
    Compound: 50S ribosomal protein L7Ae
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d1n8rh_
  • Chain 'I':
    Compound: Acidic ribosomal protein P0 homolog
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d1n8ri_
  • Chain 'J':
    Compound: 50S ribosomal protein L10e
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed):
    • PDB 1N8R (0-166)
    Domains in SCOPe 2.01: d1n8rj_
  • Chain 'K':
    Compound: 50S ribosomal protein L13P
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d1n8rk_
  • Chain 'L':
    Compound: 50S ribosomal protein L14P
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d1n8rl_
  • Chain 'M':
    Compound: 50S ribosomal protein L15P
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d1n8rm_
  • Chain 'N':
    Compound: 50S ribosomal protein L15e
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed):
    • PDB 1N8R (0-193)
    Domains in SCOPe 2.01: d1n8rn_
  • Chain 'O':
    Compound: 50S ribosomal protein L18P
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d1n8ro_
  • Chain 'P':
    Compound: 50S ribosomal protein L18e
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d1n8rp_
  • Chain 'Q':
    Compound: 50S ribosomal protein L19e
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d1n8rq_
  • Chain 'R':
    Compound: 50S ribosomal protein L21e
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d1n8rr_
  • Chain 'S':
    Compound: 50S ribosomal protein L22P
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d1n8rs_
  • Chain 'T':
    Compound: 50S ribosomal protein L23P
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d1n8rt_
  • Chain 'U':
    Compound: 50S ribosomal protein L24P
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d1n8ru_
  • Chain 'V':
    Compound: 50S ribosomal protein L24e
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d1n8rv_
  • Chain 'W':
    Compound: 50S ribosomal protein L29P
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d1n8rw_
  • Chain 'X':
    Compound: 50S ribosomal protein L30P
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d1n8rx_
  • Chain 'Y':
    Compound: 50S ribosomal protein L31e
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d1n8ry_
  • Chain 'Z':
    Compound: 50S ribosomal protein L32e
    Species: Haloarcula marismortui [TaxId:2238]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d1n8rz_
  • Heterogens: VIR, MG, K, NA, CL, CD, HOH

PDB Chain Sequences:

  • Chain '1':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1n8r1 (1:)
    rtgrfgpryglkirvrvadveikhkkkhkcpvcgfkklkragtgiwmcghcgykiaggcy
    qpetvagkavmka
    

  • Chain '2':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1n8r2 (2:)
    tgagtpsqgkknttthtkcrrcgeksyhtkkkvcsscgfgksakrrdyewqskage
    

  • Chain '3':
    Sequence, based on SEQRES records: (download)
    >1n8r3 (3:)
    gkkskatkkrlakldnqnsrvpawvmlktdevqrnhkrrhwrrndtde
    

    Sequence, based on observed residues (ATOM records): (download)
    >1n8r3 (3:)
    gkkskatkkrlakldnqnsrvpawvmlktdernhkrrhwrrndtde
    

  • Chain '4':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1n8r4 (4:)
    mqmprrfntycphcnehqehevekvrsgrqtgmkwidrqrernsgigndgkfskvpggdk
    ptkktdlkyrcgecgkahlregwragrlefqe
    

  • Chain 'A':
    No sequence available.

  • Chain 'B':
    No sequence available.

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >1n8rC (C:)
    grriqgqrrgrgtstfrapshrykadlehrkvedgdviagtvvdiehdparsapvaavef
    edgdrrlilapegvgvgdelqvgvdaeiapgntlplaeipegvpvcnvesspgdggkfar
    asgvnaqllthdrnvavvklpsgemkrldpqcratigvvggggrtdkpfvkagnkhhkmk
    argtkwpnvrgvamnavdhpfggggrqhpgkpksisrnappgrkvgdiaskrtgrggne
    

    Sequence, based on observed residues (ATOM records): (download)
    >1n8rC (C:)
    grriqgqrrgrgtstfrapshrykadlehrkvedgdviagtvvdiehdparsapvaavef
    edgdrrlilapegvgvgdelqvgvdaeiapgntlplaeipegvpvcnvesspgdggkfar
    asgvnaqllthdrnvavvklpsgemkrldpqcratigvvggggrtdkpfvkagnkhhkmk
    argtkwpnvrgvamnavdhpfggggrqhpgkpksisrnappgrkvgdiaskrtgrgg
    

  • Chain 'D':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1n8rD (D:)
    pqpsrprkgslgfgprkrstsetprfnswpsddgqpgvqgfagykagmthvvlvndepns
    pregmeetvpvtvietppmravalrayedtpygqrpltevwtdefhseldrtldvpedhd
    pdaaeeqirdaheagdlgdlrlithtvpdavpsvpkkkpdvmetrvgggsvsdrldhald
    ivedggehamndifrageyadvagvtkgkgtqgpvkrwgvqkrkgkharqgwrrrignlg
    pwnpsrvrstvpqqgqtgyhqrtelnkrlidigegdeptvdggfvnygevdgpytlvkgs
    vpgpdkrlvrfrpavrpndqprldpevryvsnesnqg
    

  • Chain 'E':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1n8rE (E:)
    mqatiydldgntdgevdlpdvfetpvrsdligkavraaqanrkqdygsdeyaglrtpaes
    fgsgrgqahvpkldgrarrvpqavkgrsahppktekdrsldlndkerqlavrsalaatad
    adlvadrghefdrdevpvvvsddfedlvktqevvsllealdvhadidradetkikagqgs
    argrkyrrpasilfvtsdepstaarnlagadvatasevntedlapggapgrltvftesal
    aevaer
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >1n8rF (F:)
    ssesesggdfhemrepriekvvvhmgighggrdlanaedilgeitgqmpvrtkakrtvge
    fdiregdpigakvtlrdemaeeflqtalplaelatsqfddtgnfsfgveehtefpsqeyd
    psigiygldvtvnlvrpgyrvakrdkasrsiptkhrlnpadavafiestydvevse
    

    Sequence, based on observed residues (ATOM records): (download)
    >1n8rF (F:)
    fhemrepriekvvvhmgighanaedilgeitgqmpvrtkakrtvgefdiregdpigakvt
    lrdemaeeflqtalplaelatsqfddtgnfsfgldvtvnlvrpgyrvakrdkasrsiptk
    hrlnpadavafiestydvev
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >1n8rG (G:)
    prveleipedvdaeqdhlditvegdngsvtrrlwypdidvsvdgdtvviesdednaktms
    tigtfqshienmfhgvtegweygmevfyshfpmqvnvegdevvienflgekaprrttihg
    dtdveidgeeltvsgpdieavgqtaadieqltrindkdvrvfqdgvyitrkpnrgda
    

    Sequence, based on observed residues (ATOM records): (download)
    >1n8rG (G:)
    prveleipedvdaeqdhlditvegdngsvtrrlwypdidvsvdgdtvviesdednaktms
    tigtfqshienmfhgvtegweygmevfyshfpmqvnvegdevvienflgekaprrttihg
    dtdveidgeeltvsgpdieavgqtaadieqltrindkdvrvfqdgvyitrkp
    

  • Chain 'H':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1n8rH (H:)
    pvyvdfdvpadleddalealevardtgavkkgtnettksiergsaelvfvaedvqpeeiv
    mhipeladekgvpfifveqqddlghaaglevgsaaaavtdagaaatvleeiadkveelr
    

  • Chain 'I':
    Sequence, based on SEQRES records: (download)
    >1n8rI (I:)
    msaeserktetipewkqeevdaivemiesyesvgvvniagipsrqlqdmrrdlhgtaelr
    vsrntlleralddvddgledlngyitgqvgligtddnpfslfqeleasktpapigageva
    pndivipegdtgvdpgpfvgelqsvgadariqegsiqvlsdstvldtgeevsqelsnvln
    elgiepkevgldlravfadgvlfepeeleldideyrsdiqaaagrafnlsvnadyptatt
    aptmlqsdrgnakslalqaaiedpevvpdlvskadaqvralasqiddeealpeelqgvea
    dvateeptddqdddtaseddadaddaaeeadddddddedagdalgamf
    

    Sequence, based on observed residues (ATOM records): (download)
    >1n8rI (I:)
    ipewkqeevdaivemiesrntlleraldd
    

  • Chain 'J':
    Sequence, based on SEQRES records: (download)
    >1n8rJ (J:)
    kpgamyrnsskpaytrreyisgipgkkiaqfdmgnngagptypaqvelvvekpvqirhna
    leaarvaanryvqnsgaaanykfrirkfpfhvirenkaaaaaaaaaaadgmrapfgkpvg
    taarvhganhifiawvnpdpnveeawrrakmkvtptinidsspagna
    

    Sequence, based on observed residues (ATOM records): (download)
    >1n8rJ (J:)
    kpgamyrnsskpaytrreyisgipgkkiaqfdmgnngagptypaqvelvvekpvqirhna
    leaarvaanryvqnsgaaanykfrirkfpfhvirenkdgmrapfgkpvgtaarvhganhi
    fiawvnpdpnveeawrrakmkvtptinidsspagna
    

  • Chain 'K':
    Sequence, based on SEQRES records: (download)
    >1n8rK (K:)
    msvaefdadvivdardcimgrvasqvaeqaldgetvavvnaeravitgreeqivekyekr
    vdigndngyfypkrpdgifkrtirgmlphkkqrgreafesvrvylgnpydedgevldgts
    ldrlsnikfvtlgeisetlganktw
    

    Sequence, based on observed residues (ATOM records): (download)
    >1n8rK (K:)
    aefdadvivdardcimgrvasqvaeqaldgetvavvnaeravitgreeqivekyekrvdi
    gndngyfypkrpdgifkrtirgmlphkkqrgreafesvrvylgnpydedgevldgtsldr
    lsnikfvtlgeisetlganktw
    

  • Chain 'L':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1n8rL (L:)
    mealgadvtqglekgslitcadntgarelkvisvhgysgtknrhpkaglgdkitvsvtkg
    tpemrrqvleavvvrqrkpirrpdgtrvkfednaavivdenedprgtelkgpiarevaqr
    fgsvasaatmiv
    

  • Chain 'M':
    Sequence, based on SEQRES records: (download)
    >1n8rM (M:)
    tskkkrqrgsrthgggshknrrgaghrggrgdagrdkhefhnheplgksgfkrpqkvqee
    aatidvreidenvtllaaddvaevedggfrvdvrdvveeaddadyvkvlgagqvrheltl
    iaddfsegarekvegaggsveltdlgeerqaeaeetedadadee
    

    Sequence, based on observed residues (ATOM records): (download)
    >1n8rM (M:)
    tskkkrqrgsrthgggshknrrgaghrggrgdagrdkhefhnheplgksgfkrpqkvqee
    aatidvreidenvtllaaddvaefrvdvrdvveeaddadyvkvlgagqvrheltliaddf
    segarekvegaggsveltdlgeerq
    

  • Chain 'N':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1n8rN (N:)
    arsaysyireawkrpkegqiaelmwhrmqewrnepavvrierptrldrarslgykakqgi
    ivvrvairkgssrrtrfnkgrrskrmmvnritrkkniqriaeeranrkfpnlrvlnsysv
    gedgrhkwhevilidpdhpaiksddqlswisrtrhrlrtfrgltsagrrcrglrgqgkgs
    ekvrpslrvngaka
    

  • Chain 'O':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1n8rO (O:)
    atgprykvpmrrrreartdyhqrlrllksgkprlvarksnkhvraqlvtlgpngddtlas
    ahssdlaeygweaptgnmpsayltgllaglraqeagveeavldiglnsptpgskvfaiqe
    gaidagldiphnddvladwqrtrgahiaeydeqleeplysgdfdaadlpehfdelretll
    dgdiel
    

  • Chain 'P':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1n8rP (P:)
    sktnprlssliadlksaarssggavwgdvaerlekprrthaevnlgrieryaqedetvvv
    pgkvlgsgvlqkdvtvaavdfsgtaetkidqvgeavsleqaiennpegshvrvir
    

  • Chain 'Q':
    Sequence, based on SEQRES records: (download)
    >1n8rQ (Q:)
    tdlsaqkrlaadvldvgknrvwfnperqgdiadaitredvrelvdegaiqakdkkgnsrg
    rarerqkkrakghqkgagsrkgkagarqnskedwesriraqrtklrelrdegtlsssqyr
    dlydkagggefdsvadleryidanhgda
    

    Sequence, based on observed residues (ATOM records): (download)
    >1n8rQ (Q:)
    tdlsaqkrlaadvldvgknrvwfnperqgdiadaitredvrelvdegaiqakdkkgnsrg
    rarerqkkrakghqkgagsrkgkagarqnskedwesriraqrtklrelrdegtlsssqyr
    dlydkagggefdsvadleryida
    

  • Chain 'R':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1n8rR (R:)
    pssngplegtrgklknkprdrgtsppqraveefddgekvhlkidpsvpngrfhprfdgqt
    gtvegkqgdaykvdivdggkektiivtaahlrrqe
    

  • Chain 'S':
    Sequence, based on SEQRES records: (download)
    >1n8rS (S:)
    gisysveadpdttakamlrerqmsfkhskaiareikgktageavdyleaviegdqpvpfk
    qhnsgvghkskvdgwdagrypekaskafldllenavgnadhqgfdgeamtikhvaahkvg
    eqqgrkpramgrasawnspqvdvelileepeved
    

    Sequence, based on observed residues (ATOM records): (download)
    >1n8rS (S:)
    gisysveadpdttakamlrerqmsfkhskaiareikgktageavdyleaviegdqpvpfk
    qhnsgvghkskvdgwdagrypekaskafldllenavgnadhqgfdgeamtikhvaahkvg
    eqqgrkpramgrasawnspqvdvelileep
    

  • Chain 'T':
    Sequence, based on SEQRES records: (download)
    >1n8rT (T:)
    swdvikhphvtekamndmdfqnklqfavddraskgevadaveeqydvtveqvntqntmdg
    ekkavvrlsedddaqevasrigvf
    

    Sequence, based on observed residues (ATOM records): (download)
    >1n8rT (T:)
    swdvikhphvtekamndmdfqnklqfavddraskgevadaveeqydvtveqvntqntmdg
    ekkavvrlsedddaqevasri
    

  • Chain 'U':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1n8rU (U:)
    skqpdkqrksqrraplherhkqvratlsadlreeygqrnvrvnagdtvevlrgdfageeg
    evinvdldkavihvedvtlektdgeevprpldtsnvrvtdldledekrearleseddsa
    

  • Chain 'V':
    Sequence, based on SEQRES records: (download)
    >1n8rV (V:)
    prtrecdycgtdiepgtgtmfvhkdgatthfcsskcennadlgrearnlewtdtargeag
    eaedea
    

    Sequence, based on observed residues (ATOM records): (download)
    >1n8rV (V:)
    recdycgtdiepgtgtmfvhkdgatthfcsskcennadlgrearnlewtdtar
    

  • Chain 'W':
    Sequence, based on SEQRES records: (download)
    >1n8rW (W:)
    tvlhvqeirdmtpaereaelddlktellnaravqaaggapenpgrikelrkaiariktiq
    geegdlqene
    

    Sequence, based on observed residues (ATOM records): (download)
    >1n8rW (W:)
    tvlhvqeirdmtpaereaelddlktellnaravqaaggapenpgrikelrkaiariktiq
    geegd
    

  • Chain 'X':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1n8rX (X:)
    mhalvqlrgevnmhtdiqdtlemlnihhvnhctlvpetdayrgmvakvndfvafgepsqe
    tletvlatraeplegdadvddewvaehtdyddisglafallseettlreqglsptlrlhp
    prgghdgvkhpvkeggqlgkhdtegiddlleamr
    

  • Chain 'Y':
    Sequence, based on SEQRES records: (download)
    >1n8rY (Y:)
    sasdfeervvtiplrdaraepnhkradkamilirehlakhfsvdedavrldpsineaawa
    rgrantpskirvraarfeeegeaiveaetae
    

    Sequence, based on observed residues (ATOM records): (download)
    >1n8rY (Y:)
    ervvtiplrdaraepnhkradkamilirehlakhfsvdedavrldpsineaawargrant
    pskirvraarfeeegeaiveae
    

  • Chain 'Z':
    Sequence, based on SEQRES records: (download)
    >1n8rZ (Z:)
    adneedveaeeeyteltdisgvgpskaeslreagfesvedvrgadqsaladvsgignala
    arikadvggleveseteaeveeeggeeapdedvetelqargltektpdlsdedarlltqr
    hrvgkpqfnrqdhhkkkrvstswrkprgqlskqrrgikgkgdtveagfrsptavrgkhps
    gfeevrvhnvddlegvdgdteavriaskvgarkrerieeeaedagirvlnptyvevevse
    

    Sequence, based on observed residues (ATOM records): (download)
    >1n8rZ (Z:)
    telqargltektpdlsdedarlltqrhrvgkpqfnrqdhhkkkrvstswrkprgqlskqr
    rgikgkgdtveagfrsptavrgkhpsgfeevrvhnvddlegvdgdteavriaskvgarkr
    erieeeaedagirvlnptyvev