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PDB entry 4KD8

View 4KD8 on RCSB PDB site
Description: 70s ribosome translocation intermediate fa-3.6a containing elongation factor efg/fusidic acid/gdp, mrna, and trna bound in the pe*/e state. this entry contains the 30s ribosomal subunit a. the 50s subunit a can be found in 4kd9. molecule b in the same asymmetric unit is deposited as 4kda (30s) and 4kdb (50s).
Deposited on 2013-04-24, released 2013-07-03
The last revision was dated 2014-12-10, with a file datestamp of 2014-12-05.
Experiment type: XRAY
Resolution: 3.5 Å
R-factor: 0.284
AEROSPACI score: 0.03 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: ribosomal RNA 16S
    Species: Thermus thermophilus [TaxId:262724]
  • Chain 'B':
    Compound: 30S ribosomal protein S2
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
  • Chain 'C':
    Compound: 30S ribosomal protein S3
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
  • Chain 'D':
    Compound: 30S ribosomal protein S4
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
  • Chain 'E':
    Compound: 30S ribosomal protein S5
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
  • Chain 'F':
    Compound: 30S ribosomal protein S6
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
  • Chain 'G':
    Compound: 30S ribosomal protein S7
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
  • Chain 'H':
    Compound: 30S ribosomal protein S8
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
  • Chain 'I':
    Compound: 30S ribosomal protein S9
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P62669 (0-126)
      • conflict (56)
  • Chain 'J':
    Compound: 30S ribosomal protein S10
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
  • Chain 'K':
    Compound: 30S ribosomal protein S11
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
  • Chain 'L':
    Compound: 30S ribosomal protein S12
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
  • Chain 'M':
    Compound: 30S ribosomal protein S13
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
  • Chain 'N':
    Compound: 30s ribosomal protein s14 type z
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
  • Chain 'O':
    Compound: 30S ribosomal protein S15
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
  • Chain 'P':
    Compound: 30S ribosomal protein S16
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
  • Chain 'Q':
    Compound: 30S ribosomal protein S17
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P62658 (0-99)
      • conflict (94)
  • Chain 'R':
    Compound: 30S ribosomal protein S18
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
  • Chain 'S':
    Compound: 30S ribosomal protein S19
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
  • Chain 'T':
    Compound: 30S ribosomal protein S20
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P62661 (0-98)
      • conflict (33)
  • Chain 'U':
    Compound: Viomycin
    Species: Streptomyces [TaxId:1883]
    Database cross-references and differences (RAF-indexed):
    • NOR NOR00633 (0-5)
  • Chain 'V':
    Compound: messenger RNA
    Species: Thermus thermophilus [TaxId:262724]
  • Chain 'W':
    Compound: transfer RNA
    Species: Escherichia coli [TaxId:562]
  • Chain 'Y':
    Compound: Elongation factor G
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q72I01 (0-686)
      • conflict (125)
      • conflict (222)
  • Heterogens: FUA, GDP, MG

PDB Chain Sequences:
This PDB entry is not classified in SCOPe 2.06, so the chain sequences below are not included in the ASTRAL sequence sets.

  • Chain 'A':
    No sequence available.

  • Chain 'B':
    Sequence; same for both SEQRES and ATOM records:
    >4kd8B (B:)
    vkelleagvhfgherkrwnpkfaryiyaerngihiidlqktmeelertfrfiedlamrgg
    tilfvgtkkqaqdivrmeaeragmpyvnqrwlggmltnfktisqrvhrleelealfaspe
    ieerpkkeqvrlkhelerlqkylsgfrllkrlpdaifvvdptkeaiavrearklfipvia
    ladtdsdpdlvdyiipgnddairsiqlilsravdliiqarggvvepspsyalvqe
    

  • Chain 'C':
    Sequence; same for both SEQRES and ATOM records:
    >4kd8C (C:)
    gnkihpigfrlgitrdwesrwyagkkqyrhllledqrirgllekelysaglarvdieraa
    dnvavtvhvakpgvvigrggerirvlreelakltgknvalnvqevqnpnlsaplvaqrva
    eqierrfavrraikqavqrvmesgakgakvivsgriggaeqartewaaqgrvplhtlran
    idygfalarttygvlgvkayiflgevi
    

  • Chain 'D':
    Sequence; same for both SEQRES and ATOM records:
    >4kd8D (D:)
    gryigpvcrlcrregvklylkgercyspkcamerrpyppgqhgqkrarrpsdyavrlrek
    qklrriygiserqfrnlfeeaskkkgvtgsvflgllesrldnvvyrlgfavsrrqarqlv
    rhghitvngrrvdlpsyrvrpgdeiavaeksrnlelirqnleamkgrkvgpwlsldvegm
    kgkflrlpdredlalpvneqlviefysr
    

  • Chain 'E':
    Sequence; same for both SEQRES and ATOM records:
    >4kd8E (E:)
    dfeekmilirrtarmqaggrrfrfgalvvvgdrqgrvglgfgkapevplavqkagyyarr
    nmvevplqngtipheievefgaskivlkpaapgtgviagavprailelagvtdiltkelg
    srnpiniayatmealrqlrtkadverlrkge
    

  • Chain 'F':
    Sequence; same for both SEQRES and ATOM records:
    >4kd8F (F:)
    mrryevnivlnpnldqsqlalekeiiqralenygarvekveelglrrlaypiakdpqgyf
    lwyqvempedrvndlarelrirdnvrrvmvvksqepflana
    

  • Chain 'G':
    Sequence; same for both SEQRES and ATOM records:
    >4kd8G (G:)
    arrrraevrqlqpdlvygdvlvtafinkimrdgkknlaarifydackiiqektgqeplkv
    fkqavenvkprmevrsrrvgganyqvpmevsprrqqslalrwlvqaanqrperraavria
    helmdaaegkggavkkkedvermaeanrayahyrw
    

  • Chain 'H':
    Sequence; same for both SEQRES and ATOM records:
    >4kd8H (H:)
    mltdpiadmltrirnatrvykestdvpasrfkeeilrilaregfikgyervdvdgkpylr
    vylkygprrqgpdprpeqvihhirriskpgrrvyvgvkeiprvrrglgiailstskgvlt
    drearklgvggelicevw
    

  • Chain 'I':
    Sequence; same for both SEQRES and ATOM records:
    >4kd8I (I:)
    eqyygtgrrkeavarvflrpgngkvtvngqdfneyfqglvravaaleplravdalghfda
    yitvrgggksgqidaiklgiaralvqynpdyraklkplgfltrdarvverkkygkhkarr
    apqyskr
    

  • Chain 'J':
    Sequence; same for both SEQRES and ATOM records:
    >4kd8J (J:)
    kiriklrgfdhktldasaqkiveaarrsgaqvsgpiplptrvrrftvirgpfkhkdsreh
    felrthnrlvdiinpnrktieqlmtldlptgveieiktv
    

  • Chain 'K':
    Sequence; same for both SEQRES and ATOM records:
    >4kd8K (K:)
    krqvasgrayihasynntivtitdpdgnpitwssggvigykgsrkgtpyaaqlaaldaak
    kamaygmqsvdvivrgtgagreqairalqasglqvksivddtpvphngcrpkkkfrkas
    

  • Chain 'L':
    Sequence; same for both SEQRES and ATOM records:
    >4kd8L (L:)
    ptinqlvrkgrekvrkkskvpalkgapfrrgvctvvrtvtpkkpnsalrkvakvrltsgy
    evtayipgeghnlqehsvvlirggrvkdlpgvryhivrgvydaagvkdrkksrskygtkk
    pkeaa
    

  • Chain 'M':
    Sequence; same for both SEQRES and ATOM records:
    >4kd8M (M:)
    ariagveiprnkrvdvaltyiygigkarakealektginpatrvkdlteaevvrlreyve
    ntwklegelraevaanikrlmdigcyrglrhrrglpvrgqrtrtnartrkgprktvagkk
    kaprk
    

  • Chain 'N':
    Sequence; same for both SEQRES and ATOM records:
    >4kd8N (N:)
    arkaliekakrtpkfkvraytrcvrcgrarsvyrffglcriclrelahkgqlpgvrkasw
    

  • Chain 'O':
    Sequence; same for both SEQRES and ATOM records:
    >4kd8O (O:)
    pitkeekqkviqefarfpgdtgstevqvalltlrinrlsehlkvhkkdhhshrgllmmvg
    qrrrllrylqredperyralieklgirg
    

  • Chain 'P':
    Sequence; same for both SEQRES and ATOM records:
    >4kd8P (P:)
    mvkirlarfgskhnphyrivvtdarrkrdgkyiekigyydprkttpdwlkvdverarywl
    svgaqptdtarrllrqagvfrqea
    

  • Chain 'Q':
    Sequence; same for both SEQRES and ATOM records:
    >4kd8Q (Q:)
    pkkvltgvvvsdkmqktvtvlverqfphplygkvikrskkylahdpeekyklgdvveiie
    srpiskrkrfrvlrlvesgrmdlvekylirrqnyeslskr
    

  • Chain 'R':
    Sequence; same for both SEQRES and ATOM records:
    >4kd8R (R:)
    kakvkatlgefdlrdyrnvevlkrflsetgkilprrrtglsakeqrilaktikrarilgl
    lpfteklvrk
    

  • Chain 'S':
    Sequence; same for both SEQRES and ATOM records:
    >4kd8S (S:)
    slkkgvfvddhllekvlelnakgekrliktwsrrstivpemvghtiavyngkqhvpvyit
    enmvghklgefaptrtyrg
    

  • Chain 'T':
    Sequence; same for both SEQRES and ATOM records:
    >4kd8T (T:)
    rnlsalkrhrqslkrrlrnkakksaiktlskkaiqlaqegkaeealkimrkaeslidkaa
    kgstlhknaaarrksrlmrkvrqlleaagapliggglsa
    

  • Chain 'U':
    Sequence; same for both SEQRES and ATOM records:
    >4kd8U (U:)
    xassxx
    

  • Chain 'V':
    No sequence available.

  • Chain 'W':
    No sequence available.

  • Chain 'Y':
    Sequence, based on SEQRES records:
    >4kd8Y (Y:)
    kveydlkrlrnigiaahidagktttterilyytgrihkigevhegaatmdfmeqerergi
    titaavttcfwkdhriniidtpghvdftieversmrvldgaivvfdssqgvepqsetvwr
    qaekykvpriafankmdktgadlwlvirtmqerlgarpvvmqlpigredtfsgiidvlrm
    kaytygndlgtdireipipeeyldqareyheklvevaadfdenimlkylegeepteeelv
    aairkgtidlkitpvflgsalknkgvqllldavvdylpspldippikgttpegevveihp
    dpngplaalafkimadpyvgrltfirvysgtltsgsyvynttkgrkervarllrmhanhr
    eeveelkagdlgavvglketitgdtlvgedaprvilesievpepvidvaiepktkadqek
    lsqalarlaeedptfrvsthpetgqtiisgmgelhleiivdrlkrefkvdanvgkpqvay
    retitkpvdvegkfirqtggrgqyghvkikveplprgsgfefvnaivggvipkeyipavq
    kgieeamqsgpligfpvvdikvtlydgsyhevdssemafkiagsmaikeavqkgdpvile
    pimrvevttpeeymgdvigdlnarrgqilgmeprgnaqvirafvplaemfgyatdlrskt
    qgrgsfvmffdhyqevpkqvqeklikg
    

    Sequence, based on observed residues (ATOM records):
    >4kd8Y (Y:)
    kveydlkrlrnigiaahidagktttterilyytgrihkigtitaavttcfwkdhriniid
    tpghvdftieversmrvldgaivvfdssqgvepqsetvwrqaekykvpriafankmdktg
    adlwlvirtmqerlgarpvvmqlpigredtfsgiidvlrmkaytygndlgtdireipipe
    eyldqareyheklvevaadfdenimlkylegeepteeelvaairkgtidlkitpvflgsa
    lknkgvqllldavvdylpspldippikgttpegevveihpdpngplaalafkimadpyvg
    rltfirvysgtltsgsyvynttkgrkervarllrmhanhreeveelkagdlgavvglket
    itgdtlvgedaprvilesievpepvidvaiepktkadqeklsqalarlaeedptfrvsth
    petgqtiisgmgelhleiivdrlkrefkvdanvgkpqvayretitkpvdvegkfirqtgg
    rgqyghvkikveplprgsgfefvnaivggvipkeyipavqkgieeamqsgpligfpvvdi
    kvtlydgsyhevdssemafkiagsmaikeavqkgdpvilepimrvevttpeeymgdvigd
    lnarrgqilgmeprgnaqvirafvplaemfgyatdlrsktqgrgsfvmffdhyqevpkqv
    qeklikg