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PDB entry 4KDB

View 4KDB 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 50s ribosomal subunit b. the 30s subunit a can be found in 4kda. molecule a in the same asymmetric unit is deposited as 4kd8 (30s) and 4kd9 (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: 0.02 (click here for full SPACI score report)

Chains and heterogens:

  • Chain '0':
    Compound: 50S ribosomal protein L27
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q72HR3 (0-83)
      • conflict (9)
  • Chain '1':
    Compound: 50S ribosomal protein L28
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q72G84 (0-92)
      • conflict (78)
  • Chain '2':
    Compound: 50S ribosomal protein L29
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
  • Chain '3':
    Compound: 50S ribosomal protein L30
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
  • Chain '4':
    Compound: 50S ribosomal protein L31
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
  • Chain '5':
    Compound: 50S ribosomal protein L32
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P62652 (0-58)
      • conflict (27)
  • Chain '6':
    Compound: 50S ribosomal protein L33
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
  • Chain '7':
    Compound: 50S ribosomal protein L34
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
  • Chain '8':
    Compound: 50S ribosomal protein L35
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
  • Chain '9':
    Compound: 50S ribosomal protein L36
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
  • Chain 'A':
    Compound: 23S ribosomal RNA
    Species: Thermus thermophilus [TaxId:262724]
  • Chain 'B':
    Compound: 5S ribosomal RNA
    Species: Thermus thermophilus [TaxId:262724]
  • Chain 'C':
    Compound: 50s ribosomal protein l1
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q72GV9 (0-227)
      • conflict (18)
      • conflict (26)
  • Chain 'D':
    Compound: 50S ribosomal protein L2
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
  • Chain 'E':
    Compound: 50S ribosomal protein L3
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
  • Chain 'F':
    Compound: 50S ribosomal protein L4
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q72I05 (0-207)
      • insertion (1-5)
  • Chain 'G':
    Compound: 50S ribosomal protein L5
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q72I16 (0-180)
      • conflict (3)
  • Chain 'H':
    Compound: 50S ribosomal protein L6
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
  • Chain 'J':
    Compound: 50s ribosomal protein l10
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
    • PDB 4KDB (0-169)
  • Chain 'K':
    Compound: 50S ribosomal protein L11
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
  • Chain 'N':
    Compound: 50S ribosomal protein L13
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
  • Chain 'O':
    Compound: 50S ribosomal protein L14
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q72I14 (0-121)
      • conflict (68)
  • Chain 'P':
    Compound: 50S ribosomal protein L15
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
  • Chain 'Q':
    Compound: 50S ribosomal protein L16
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q72I11 (0-140)
      • conflict (31)
  • Chain 'R':
    Compound: 50S ribosomal protein L17
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
  • Chain 'S':
    Compound: 50S ribosomal protein L18
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
  • Chain 'T':
    Compound: 50S ribosomal protein L19
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q72JU9 (0-137)
      • conflict (122)
      • conflict (134)
  • Chain 'U':
    Compound: 50S ribosomal protein L20
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
  • Chain 'V':
    Compound: 50S ribosomal protein L21
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
  • Chain 'W':
    Compound: 50S ribosomal protein L22
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
  • Chain 'X':
    Compound: 50S ribosomal protein L23
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
  • Chain 'Y':
    Compound: 50S ribosomal protein L24
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
  • Chain 'Z':
    Compound: 50S ribosomal protein L25
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
  • Chain 'e':
    Compound: 50S ribosomal protein L7/L12
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q72GS2 (31-101)
    • PDB 4KDB (0-101)
  • Chain 'f':
    Compound: 50S ribosomal protein L7/L12
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
    • PDB 4KDB (0-30)
  • Chain 'g':
    Compound: 50S ribosomal protein L7/L12
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
    • PDB 4KDB (0-30)
  • Chain 'h':
    Compound: 50S ribosomal protein L7/L12
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
    • PDB 4KDB (0-29)

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 '0':
    Sequence; same for both SEQRES and ATOM records:
    >4kdb0 (0:)
    ahkkglgstrngrdsqakrlgvkryegqvvragnilvrqrgtrfkpgknvgmgrdftlfa
    lvdgvvefqdrgrlgryvhvrpla
    

  • Chain '1':
    Sequence; same for both SEQRES and ATOM records:
    >4kdb1 (1:)
    kvceisgkrpivansiqrrgkakreggvgkkttgiskrrqypnlqkvrvrvagqeitfrv
    aashipkvyelverakglkleglspkeikkell
    

  • Chain '2':
    Sequence; same for both SEQRES and ATOM records:
    >4kdb2 (2:)
    klsevrkqleearklspveleklvrekkrelmelrfqasigqlsqnhkirdlkrqiarll
    tvlnekrrqna
    

  • Chain '3':
    Sequence; same for both SEQRES and ATOM records:
    >4kdb3 (3:)
    mprlkvklvkspigypkdqkaalkalglrrlqqervledtpairgnvekvahlvrvevve
    

  • Chain '4':
    Sequence; same for both SEQRES and ATOM records:
    >4kdb4 (4:)
    mkegihpklvpariicgcgnvietystkpeiyvev
    

  • Chain '5':
    Sequence; same for both SEQRES and ATOM records:
    >4kdb5 (5:)
    akhpvpkkktskarrdarrshhaltpptlvpcpeckamkpphtvcpecgyyagrkvlev
    

  • Chain '6':
    Sequence; same for both SEQRES and ATOM records:
    >4kdb6 (6:)
    vriklllecteckrrnyateknkrntpnklelrkycpwcrkhtvhrevki
    

  • Chain '7':
    Sequence; same for both SEQRES and ATOM records:
    >4kdb7 (7:)
    mkrtwqpnrrkrakthgfrarmrtpggrkvlkrrrqkgrwrltpavrkr
    

  • Chain '8':
    Sequence; same for both SEQRES and ATOM records:
    >4kdb8 (8:)
    pkmkthkgakkrvkitasgkvvamktgkrhlnwqksgkeirqkgrkfvlakpeaerikll
    lpye
    

  • Chain '9':
    Sequence; same for both SEQRES and ATOM records:
    >4kdb9 (9:)
    mkvrasvkricdkckvirrhgrvyvicenpkhkqrqg
    

  • Chain 'A':
    No sequence available.

  • Chain 'B':
    No sequence available.

  • Chain 'C':
    Sequence; same for both SEQRES and ATOM records:
    >4kdbC (C:)
    pkhgkryrallekvdpnkvytideaarlvkelatakfdetvevhaklgidprrsdqnvrg
    tvslphglgkqvrvlaiakgekikeaeeagadyvggeeiiqkildgwmdfdavvatpdvm
    gavgsklgrilgprgllpnpkagtvgfnigeiireikagriefrndktgaihapvgkasf
    ppekladnirafiraleahkpegakgtflrsvyvtttmgpsvrinphs
    

  • Chain 'D':
    Sequence; same for both SEQRES and ATOM records:
    >4kdbD (D:)
    avkkfkpytpsrrfmtvadfseitktepekslvkplkktggrnnqgritvrfrggghkrl
    yriidfkrwdkvgipakvaaieydpnrsariallhyvdgekryiiapdglqvgqqvvagp
    dapiqvgnalplrfipvgtvvhavelepkkgaklaraagtsaqiqgregdyvilrlpsge
    lrkvhgecyatvgavgnadhknivlgkagrsrwlgrrphvrgaamnpvdhphgggegrap
    rgrppaspwgwqtkglktrkrrkpssrfiiarrkk
    

  • Chain 'E':
    Sequence; same for both SEQRES and ATOM records:
    >4kdbE (E:)
    mkgilgvkvgmtrifrddravpvtvilagpcpvvqrrtpekdgytavqlgflpqnpkrvn
    rplkghfakagvepvrilreirdfnpegdtvtveifkpgervdvtgtskgrgfagvmkrw
    nfaggpdshgahkihrhpgsignrktpgrvykgkkmaghygaervtvmnlevvdvipeen
    lllvkgavpgpngglvivretkkaa
    

  • Chain 'F':
    Sequence; same for both SEQRES and ATOM records:
    >4kdbF (F:)
    mkevavyqipvlspsgrrelaadlpaeinphllwevvrwqlakrrrgtastktrgevays
    grkiwpqkhtgrarhgdigapifvgggvvfgpkprdysytlpkkvrkkglamavadrare
    gklllveafagvngktkeflawakeagldgsesvllvtgnelvrraarnlpwvvtlapeg
    lnvydivrterlvmdldawevfqnrigg
    

  • Chain 'G':
    Sequence; same for both SEQRES and ATOM records:
    >4kdbG (G:)
    pldvalkrkyyeevrpelirrfgyqnvwevprlekvvinqglgeakedarilekaaqela
    litgqkpavtrakksisnfklrkgmpiglrvtlrrdrmwiflekllnvalprirdfrgln
    pnsfdgrgnynlglreqlifpeitydmvdalrgmdiavvttaetdeearallellgfpfr
    k
    

  • Chain 'H':
    Sequence; same for both SEQRES and ATOM records:
    >4kdbH (H:)
    pkgvsvevapgrvkvkgpkgelevpvspemrvvveegvvrverpsderrhkslhgltrtl
    ianavkgvsegyskellikgigyrarlvgraleltvgfshpvvveppegitfevpeptrv
    rvsgidkqkvgqvaanirairkpsayhekgiyyagepvrlkpgkaga
    

  • Chain 'J':
    Sequence; same for both SEQRES and ATOM records:
    >4kdbJ (J:)
    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
    

  • Chain 'K':
    Sequence; same for both SEQRES and ATOM records:
    >4kdbK (K:)
    kkvvavvklqlpagkatpappvgpalgqhganimefvkafnaatanmgdaivpveitiya
    drsftfvtktppasylirkaaglekgahkpgrekvgritweqvleiakqkmpdlnttdle
    aaarmiagsarsmgvevvga
    

  • Chain 'N':
    Sequence; same for both SEQRES and ATOM records:
    >4kdbN (N:)
    mktyvpkqveprwvlidaegktlgrlatkiatllrgkhrpdwtpnvamgdfvvvvnadki
    rvtgkkleqkiytrysgypgglkkiplekmlathpervlehavkgmlpkgplgrrlfkrl
    kvyagpdhphqaqrpekl
    

  • Chain 'O':
    Sequence; same for both SEQRES and ATOM records:
    >4kdbO (O:)
    miqpqtylevadntgarkimcirvlkgsnakyatvgdvivasvkeaiprgavkegdvvka
    vvvrtkkeikrpdgsairfddnaaviinnqleprgtrvfgpvarelrekgfmkivslape
    vl
    

  • Chain 'P':
    Sequence; same for both SEQRES and ATOM records:
    >4kdbP (P:)
    dlrpnpgankrrkrvgrgpgsghgktatrghkgqksrsgglkdprrfeggrsttlmrlpk
    rgmqgqvpgeikrpryqgvnlkdlarfegevtpellvragllkkgyrlkilgegeakplk
    vvahafsksaleklkaaggepvllea
    

  • Chain 'Q':
    Sequence; same for both SEQRES and ATOM records:
    >4kdbQ (Q:)
    mlmprrmkyrkqqrgrlkgatkggdyvafgdyglvalepawitaqqieaarvamvrhfrr
    ggkifirifpdkpytkkplevrmgkgkgnvegyvavvkpgrvmfevagvteeqamealri
    aghklpiktkivrrdaydeaq
    

  • Chain 'R':
    Sequence; same for both SEQRES and ATOM records:
    >4kdbR (R:)
    rhlksgrklnrhsshrlalyrnqaksllthgritttvpkakelrgfvdhlihlakrgdlh
    arrlvlrdlqdvklvrklfdeiapryrdrqggytrvlklaerrrgdgaplalvelve
    

  • Chain 'S':
    Sequence; same for both SEQRES and ATOM records:
    >4kdbS (S:)
    kfrvrnrikrtgrlrlsvfrslkhiyaqiiddekgvtlvsasslalklkgnktevarqvg
    ralaekalalgikqvafdrgpykyhgrvkalaegaregg
    

  • Chain 'T':
    Sequence; same for both SEQRES and ATOM records:
    >4kdbT (T:)
    mnrgaliklvesryvrtdlpefrpgdtvrvsykvkegnrtriqdfegivirirrngfntt
    ftvrkvsygvgverifplhspliqkidivqrgrarraklyfirnlsdreirrklradrkr
    idqdraaeraakeeaqka
    

  • Chain 'U':
    Sequence; same for both SEQRES and ATOM records:
    >4kdbU (U:)
    praktgvvrrrkhkkilklakgywglrsksfrkaretlfaagnyayahrkrrkrdfrrlw
    ivrinaacrqhglnystfihglkkagievdrknladlavrepqvfaelverakaaqg
    

  • Chain 'V':
    Sequence; same for both SEQRES and ATOM records:
    >4kdbV (V:)
    mfaivktggkqyrvepglklrvekldaepgatvelpvlllggektvvgtpvvegasvvae
    vlghgrgkkilvskfkakvqyrrkkghrqpytellikeirg
    

  • Chain 'W':
    Sequence; same for both SEQRES and ATOM records:
    >4kdbW (W:)
    meakaiaryvrisprkvrlvvdlirgksleearnilrytnkrgayfvakvlesaaanavn
    nhdmledrlyvkaayvdegpalkrvlprargradiikkrtshitvilgekhgk
    

  • Chain 'X':
    Sequence; same for both SEQRES and ATOM records:
    >4kdbX (X:)
    taydvilapvlsekayagfaegkytfwvhpkatkteiknavetafkvkvvkvntlhvrgk
    kkrlgrylgkrpdrkkaivqvapgqkiealegl
    

  • Chain 'Y':
    Sequence; same for both SEQRES and ATOM records:
    >4kdbY (Y:)
    rvkmhvkkgdtvlvasgkykgrvgkvkevlpkkyavivegvnivkkavrvspkypqggfi
    ekeaplhaskvrpicpacgkptrvrkkflengkkirvcakcggaldt
    

  • Chain 'Z':
    Sequence; same for both SEQRES and ATOM records:
    >4kdbZ (Z:)
    yrlkayyregekpsalrragklpgvmynrhlnrkvyvdlvefdkvfrqasihhvivlelp
    dgqslptlvrqvnldkrrrrpehvdffvlsdepvemyvplrfvgtpagvraggvlqeihr
    dilvkvsprnipefievdvsgleigdslhasdlklppgvelavspeetiaavvppedvek
    laeea
    

  • Chain 'e':
    Sequence; same for both SEQRES and ATOM records:
    >4kdbe (e:)
    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxaapaeektefdvilkeagakklevikelra
    itglglkeakdlaekggpvkegvskqeaeeikkkleavgavv
    

  • Chain 'f':
    Sequence; same for both SEQRES and ATOM records:
    >4kdbf (f:)
    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
    

  • Chain 'g':
    Sequence; same for both SEQRES and ATOM records:
    >4kdbg (g:)
    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
    

  • Chain 'h':
    Sequence; same for both SEQRES and ATOM records:
    >4kdbh (h:)
    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx