PDB entry 2uxd

View 2uxd on RCSB PDB site
Description: Crystal structure of an extended tRNA anticodon stem loop in complex with its cognate mRNA CGGG in the context of the Thermus thermophilus 30S subunit.
Class: ribosome
Keywords: ribonucleoprotein, 30s ribosomal subunit, frameshift suppressor tRNA, tRNA, mRNA, codon, a site, ribosome, decoding, metal-binding, messenger RNA, ribosomal protein, RNA-binding, paromomycin, anticodon, stem-loop, frameshift, zinc-finger, rRNA-binding, tRNA-binding, transfer RNA
Deposited on 2007-03-28, released 2007-10-02
The last revision prior to the SCOPe 2.07 freeze date was dated 2012-10-10, with a file datestamp of 2012-10-05.
Experiment type: XRAY
Resolution: 3.2 Å
R-factor: 0.238
AEROSPACI score: 0.14 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: 16S ribosomal RNA
    Species: Thermus thermophilus [TaxId:300852]
  • Chain 'B':
    Compound: ribosomal protein s2
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2uxdb1
  • Chain 'C':
    Compound: ribosomal protein s3
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
    • PDB 2UXD
    • Uniprot P80372 (1-End)
  • Chain 'D':
    Compound: ribosomal protein s4
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
    • PDB 2UXD
    • Uniprot P80373 (1-208)
    Domains in SCOPe 2.07: d2uxdd1
  • Chain 'E':
    Compound: ribosomal protein s5
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2uxde1
  • Chain 'F':
    Compound: ribosomal protein s6
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2uxdf1
  • Chain 'G':
    Compound: ribosomal protein s7
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
    • PDB 2UXD
    • Uniprot P17291 (1-155)
    Domains in SCOPe 2.07: d2uxdg1
  • Chain 'H':
    Compound: ribosomal protein s8
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2uxdh1
  • Chain 'I':
    Compound: ribosomal protein s9
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P80374 (Start-127)
      • conflict (57)
    Domains in SCOPe 2.07: d2uxdi1
  • Chain 'J':
    Compound: ribosomal protein s10
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2uxdj1
  • Chain 'K':
    Compound: ribosomal protein s11
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
    • PDB 2UXD
    • Uniprot P80376 (Start-128)
    Domains in SCOPe 2.07: d2uxdk1
  • Chain 'L':
    Compound: ribosomal protein s12
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
    • PDB 2UXD
    • Uniprot Q5SHN3 (4-End)
    Domains in SCOPe 2.07: d2uxdl1
  • Chain 'M':
    Compound: ribosomal protein s13
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
    • PDB 2UXD
    • Uniprot P80377 (1-125)
    Domains in SCOPe 2.07: d2uxdm1
  • Chain 'N':
    Compound: ribosomal protein s14
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
    • PDB 2UXD
    • Uniprot Q5SHQ1 (1-60)
    Domains in SCOPe 2.07: d2uxdn1
  • Chain 'O':
    Compound: ribosomal protein s15
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
    • PDB 2UXD
    • Uniprot Q5SJ76 (1-88)
    Domains in SCOPe 2.07: d2uxdo1
  • Chain 'P':
    Compound: ribosomal protein s16
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2uxdp1
  • Chain 'Q':
    Compound: ribosomal protein s17
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
    • PDB 2UXD
      • conflict (95)
    • Uniprot Q5SHP7 (1-104)
    Domains in SCOPe 2.07: d2uxdq1
  • Chain 'R':
    Compound: ribosomal protein s18
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
    • PDB 2UXD
    • Uniprot Q5SLQ0 (Start-87)
    Domains in SCOPe 2.07: d2uxdr1
  • Chain 'S':
    Compound: ribosomal protein s19
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
    • PDB 2UXD
    • Uniprot Q5SHP2 (1-End)
    Domains in SCOPe 2.07: d2uxds1
  • Chain 'T':
    Compound: ribosomal protein s20
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
    • PDB 2UXD
      • conflict (40)
    • Uniprot P80380 (Start-105)
    Domains in SCOPe 2.07: d2uxdt1
  • Chain 'V':
    Compound: ribosomal protein thx
    Species: Thermus thermophilus [TaxId:300852]
    Database cross-references and differences (RAF-indexed):
    • PDB 2UXD
    • Uniprot Q5SIH3 (1-End)
    Domains in SCOPe 2.07: d2uxdv1
  • Chain 'X':
    Compound: anticodon stem-loop of transfer RNA with anticodon cccg
  • Chain 'Y':
    Compound: a-site messenger RNA fragment cggg
  • Heterogens: PAR, MG, K, ZN

PDB Chain Sequences:

  • Chain 'A':
    No sequence available.

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >2uxdB (B:)
    mpveitvkelleagvhfgherkrwnpkfaryiyaerngihiidlqktmeelertfrfied
    lamrggtilfvgtkkqaqdivrmeaeragmpyvnqrwlggmltnfktisqrvhrleelea
    lfaspeieerpkkeqvrlkhelerlqkylsgfrllkrlpdaifvvdptkeaiavrearkl
    fipvialadtdsdpdlvdyiipgnddairsiqlilsravdliiqarggvvepspsyalvq
    eaeatetpegesevea
    

    Sequence, based on observed residues (ATOM records): (download)
    >2uxdB (B:)
    vkelleagvhfgherkrwnpkfaryiyaerngihiidlqktmeelertfrfiedlamrgg
    tilfvgtkkqaqdivrmeaeragmpyvnqrwlggmltnfktisqrvhrleelealfaspe
    ieerpkkeqvrlkhelerlqkylsgfrllkrlpdaifvvdptkeaiavrearklfipvia
    ladtdsdpdlvdyiipgnddairsiqlilsravdliiqarggvvepspsyalvqe
    

  • Chain 'C':
    No sequence available.

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >2uxdD (D:)
    mgryigpvcrlcrregvklylkgercyspkcamerrpyppgqhgqkrarrpsdyavrlre
    kqklrriygiserqfrnlfeeaskkkgvtgsvflgllesrldnvvyrlgfavsrrqarql
    vrhghitvngrrvdlpsyrvrpgdeiavaeksrnlelirqnleamkgrkvgpwlsldveg
    mkgkflrlpdredlalpvneqlviefysr
    

    Sequence, based on observed residues (ATOM records): (download)
    >2uxdD (D:)
    gryigpvcrlcrregvklylkgercyspkcamerrpyppgqhgqkrarrpsdyavrlrek
    qklrriygiserqfrnlfeeaskkkgvtgsvflgllesrldnvvyrlgfavsrrqarqlv
    rhghitvngrrvdlpsyrvrpgdeiavaeksrnlelirqnleamkgrkvgpwlsldvegm
    kgkflrlpdredlalpvneqlviefysr
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >2uxdE (E:)
    mpetdfeekmilirrtarmqaggrrfrfgalvvvgdrqgrvglgfgkapevplavqkagy
    yarrnmvevplqngtipheievefgaskivlkpaapgtgviagavprailelagvtdilt
    kelgsrnpiniayatmealrqlrtkadverlrkgeahaqaqg
    

    Sequence, based on observed residues (ATOM records): (download)
    >2uxdE (E:)
    dfeekmilirrtarmqaggrrfrfgalvvvgdrqgrvglgfgkapevplavqkagyyarr
    nmvevplqngtipheievefgaskivlkpaapgtgviagavprailelagvtdiltkelg
    srnpiniayatmealrqlrtkadverlrkge
    

  • Chain 'F':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2uxdF (F:)
    mrryevnivlnpnldqsqlalekeiiqralenygarvekveelglrrlaypiakdpqgyf
    lwyqvempedrvndlarelrirdnvrrvmvvksqepflana
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >2uxdG (G:)
    marrrraevrqlqpdlvygdvlvtafinkimrdgkknlaarifydackiiqektgqeplk
    vfkqavenvkprmevrsrrvgganyqvpmevsprrqqslalrwlvqaanqrperraavri
    ahelmdaaegkggavkkkedvermaeanrayahyrw
    

    Sequence, based on observed residues (ATOM records): (download)
    >2uxdG (G:)
    arrrraevrqlqpdlvygdvlvtafinkimrdgkknlaarifydackiiqektgqeplkv
    fkqavenvkprmevrsrrvgganyqvpmevsprrqqslalrwlvqaanqrperraavria
    helmdaaegkggavkkkedvermaeanrayahyrw
    

  • Chain 'H':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2uxdH (H:)
    mltdpiadmltrirnatrvykestdvpasrfkeeilrilaregfikgyervdvdgkpylr
    vylkygprrqgpdprpeqvihhirriskpgrrvyvgvkeiprvrrglgiailstskgvlt
    drearklgvggelicevw
    

  • Chain 'I':
    Sequence, based on SEQRES records: (download)
    >2uxdI (I:)
    meqyygtgrrkeavarvflrpgngkvtvngqdfneyfqglvravaaleplravdalgrfd
    ayitvrgggksgqidaiklgiaralvqynpdyraklkplgfltrdarvverkkygkhkar
    rapqyskr
    

    Sequence, based on observed residues (ATOM records): (download)
    >2uxdI (I:)
    eqyygtgrrkeavarvflrpgngkvtvngqdfneyfqglvravaaleplravdalgrfda
    yitvrgggksgqidaiklgiaralvqynpdyraklkplgfltrdarvverkkygkhkarr
    apqyskr
    

  • Chain 'J':
    Sequence, based on SEQRES records: (download)
    >2uxdJ (J:)
    mpkiriklrgfdhktldasaqkiveaarrsgaqvsgpiplptrvrrftvirgpfkhkdsr
    ehfelrthnrlvdiinpnrktieqlmtldlptgveieiktvgggr
    

    Sequence, based on observed residues (ATOM records): (download)
    >2uxdJ (J:)
    kiriklrgfdhktldasaqkiveaarrsgaqvsgpiplptrvrrftvirgpfkhkdsreh
    felrthnrlvdiinpnrktieqlmtldlptgveieiktv
    

  • Chain 'K':
    Sequence, based on SEQRES records: (download)
    >2uxdK (K:)
    makkpskkkvkrqvasgrayihasynntivtitdpdgnpitwssggvigykgsrkgtpya
    aqlaaldaakkamaygmqsvdvivrgtgagreqairalqasglqvksivddtpvphngcr
    pkkkfrkas
    

    Sequence, based on observed residues (ATOM records): (download)
    >2uxdK (K:)
    krqvasgrayihasynntivtitdpdgnpitwssggvigykgsrkgtpyaaqlaaldaak
    kamaygmqsvdvivrgtgagreqairalqasglqvksivddtpvphngcrpkkkfrkas
    

  • Chain 'L':
    Sequence, based on SEQRES records: (download)
    >2uxdL (L:)
    mvalptinqlvrkgrekvrkkskvpalkgapfrrgvctvvrtvtpkkpnsalrkvakvrl
    tsgyevtayipgeghnlqehsvvlirggrvkdlpgvryhivrgvydaagvkdrkksrsky
    gtkkpkeaaktaakk
    

    Sequence, based on observed residues (ATOM records): (download)
    >2uxdL (L:)
    ptinqlvrkgrekvrkkskvpalkgapfrrgvctvvrtvtpkkpnsalrkvakvrltsgy
    evtayipgeghnlqehsvvlirggrvkdlpgvryhivrgvydaagvkdrkksrskygtkk
    pkeaa
    

  • Chain 'M':
    Sequence, based on SEQRES records: (download)
    >2uxdM (M:)
    mariagveiprnkrvdvaltyiygigkarakealektginpatrvkdlteaevvrlreyv
    entwklegelraevaanikrlmdigcyrglrhrrglpvrgqrtrtnartrkgprktvagk
    kkaprk
    

    Sequence, based on observed residues (ATOM records): (download)
    >2uxdM (M:)
    ariagveiprnkrvdvaltyiygigkarakealektginpatrvkdlteaevvrlreyve
    ntwklegelraevaanikrlmdigcyrglrhrrglpvrgqrtrtnartrkgprktvagkk
    kaprk
    

  • Chain 'N':
    Sequence, based on SEQRES records: (download)
    >2uxdN (N:)
    markaliekakrtpkfkvraytrcvrcgrarsvyrffglcriclrelahkgqlpgvrkas
    w
    

    Sequence, based on observed residues (ATOM records): (download)
    >2uxdN (N:)
    arkaliekakrtpkfkvraytrcvrcgrarsvyrffglcriclrelahkgqlpgvrkasw
    

  • Chain 'O':
    Sequence, based on SEQRES records: (download)
    >2uxdO (O:)
    mpitkeekqkviqefarfpgdtgstevqvalltlrinrlsehlkvhkkdhhshrgllmmv
    gqrrrllrylqredperyralieklgirg
    

    Sequence, based on observed residues (ATOM records): (download)
    >2uxdO (O:)
    pitkeekqkviqefarfpgdtgstevqvalltlrinrlsehlkvhkkdhhshrgllmmvg
    qrrrllrylqredperyralieklgirg
    

  • Chain 'P':
    Sequence, based on SEQRES records: (download)
    >2uxdP (P:)
    mvkirlarfgskhnphyrivvtdarrkrdgkyiekigyydprkttpdwlkvdverarywl
    svgaqptdtarrllrqagvfrqearega
    

    Sequence, based on observed residues (ATOM records): (download)
    >2uxdP (P:)
    mvkirlarfgskhnphyrivvtdarrkrdgkyiekigyydprkttpdwlkvdverarywl
    svgaqptdtarrllrqagvfrqea
    

  • Chain 'Q':
    Sequence, based on SEQRES records: (download)
    >2uxdQ (Q:)
    mpkkvltgvvvsdkmqktvtvlverqfphplygkvikrskkylahdpeekyklgdvveii
    esrpiskrkrfrvlrlvesgrmdlvekylirrqnyqslskrggka
    

    Sequence, based on observed residues (ATOM records): (download)
    >2uxdQ (Q:)
    pkkvltgvvvsdkmqktvtvlverqfphplygkvikrskkylahdpeekyklgdvveiie
    srpiskrkrfrvlrlvesgrmdlvekylirrqnyqslskrggka
    

  • Chain 'R':
    Sequence, based on SEQRES records: (download)
    >2uxdR (R:)
    mstknakpkkeaqrrpsrkakvkatlgefdlrdyrnvevlkrflsetgkilprrrtglsa
    keqrilaktikrarilgllpfteklvrk
    

    Sequence, based on observed residues (ATOM records): (download)
    >2uxdR (R:)
    psrkakvkatlgefdlrdyrnvevlkrflsetgkilprrrtglsakeqrilaktikrari
    lgllpfteklvrk
    

  • Chain 'S':
    Sequence, based on SEQRES records: (download)
    >2uxdS (S:)
    mprslkkgvfvddhllekvlelnakgekrliktwsrrstivpemvghtiavyngkqhvpv
    yitenmvghklgefaptrtyrghgkeakatkkk
    

    Sequence, based on observed residues (ATOM records): (download)
    >2uxdS (S:)
    prslkkgvfvddhllekvlelnakgekrliktwsrrstivpemvghtiavyngkqhvpvy
    itenmvghklgefaptrtyrg
    

  • Chain 'T':
    Sequence, based on SEQRES records: (download)
    >2uxdT (T:)
    maqkkpkrnlsalkrhrqslkrrlrnkakksaiktlskkavqlaqegkaeealkimrkae
    slidkaakgstlhknaaarrksrlmrkvrqlleaagapliggglsa
    

    Sequence, based on observed residues (ATOM records): (download)
    >2uxdT (T:)
    rnlsalkrhrqslkrrlrnkakksaiktlskkavqlaqegkaeealkimrkaeslidkaa
    kgstlhknaaarrksrlmrkvrqlleaagapliggglsa
    

  • Chain 'V':
    Sequence, based on SEQRES records: (download)
    >2uxdV (V:)
    mgkgdrrtrrgkiwrgtygkyrprkkk
    

    Sequence, based on observed residues (ATOM records): (download)
    >2uxdV (V:)
    gkgdrrtrrgkiwrgtygkyrprkk
    

  • Chain 'X':
    No sequence available.

  • Chain 'Y':
    No sequence available.