SCOPe Funding Alert: SCOPe support from the NIH ended in April 2016. John-Marc Chandonia is the primary maintainer and has continued to develop SCOPe using vacation time. Three proposals to the NIH for continued funding have been unsuccessful. If our current NIH proposal is not funded, SCOPe will shut down permanently in Summer 2017 as Dr. Chandonia will need to seek a new position.
You accessed the SCOPe website through a deprecated URL; see Help for SCOPe 2.01 for more info on linking to SCOPe.
Showing results for SCOPe 2.06; you can access the page in SCOP 1.75 here.

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