PDB entry 3d5b

View 3d5b on RCSB PDB site
Description: Structural basis for translation termination on the 70S ribosome. This file contains the 50S subunit of one 70S ribosome. The entire crystal structure contains two 70S ribosomes as described in remark 400.
Class: ribosome
Keywords: Ribosome, Ribonucleoprotein, Ribosomal protein, RNA-binding, rRNA-binding, tRNA-binding, Metal-binding
Deposited on 2008-05-16, released 2008-10-07
The last revision prior to the SCOPe 2.07 freeze date was dated 2014-12-10, with a file datestamp of 2014-12-05.
Experiment type: XRAY
Resolution: 3.21 Å
R-factor: 0.292
AEROSPACI score: 0.05 (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):
  • Chain '1':
    Compound: 50S ribosomal protein L28
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
  • 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):
  • Chain '6':
    Compound: 50S ribosomal protein L33
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3d5b61
  • Chain '7':
    Compound: 50S ribosomal protein L34
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3d5b71
  • Chain '8':
    Compound: 50S ribosomal protein L35
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
  • Chain 'A':
    Compound: 23s rRNA
    Species: Thermus thermophilus [TaxId:262724]
  • Chain 'B':
    Compound: 5s rRNA
    Species: Thermus thermophilus [TaxId:262724]
  • 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): Domains in SCOPe 2.07: d3d5be1
  • Chain 'F':
    Compound: 50S ribosomal protein L4
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
  • Chain 'G':
    Compound: 50S ribosomal protein L5
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
  • Chain 'H':
    Compound: 50S ribosomal protein L6
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3d5bh1, d3d5bh2
  • Chain 'I':
    Compound: 50S ribosomal protein L9
    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):
  • Chain 'N':
    Compound: 50S ribosomal protein L13
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3d5bn1
  • Chain 'O':
    Compound: 50S ribosomal protein L14
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3d5bo1
  • Chain 'P':
    Compound: 50S ribosomal protein L15
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3d5bp1
  • Chain 'Q':
    Compound: 50S ribosomal protein L16
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed):
  • 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):
  • Chain 'U':
    Compound: 50S ribosomal protein L20
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3d5bu1
  • Chain 'V':
    Compound: 50S ribosomal protein L21
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3d5bv1
  • 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): Domains in SCOPe 2.07: d3d5by1
  • Chain 'Z':
    Compound: 50S ribosomal protein L25
    Species: Thermus thermophilus [TaxId:262724]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d3d5bz1
  • Heterogens: MG

PDB Chain Sequences:

  • Chain '0':
    No sequence available.

  • Chain '1':
    No sequence available.

  • Chain '2':
    No sequence available.

  • Chain '3':
    No sequence available.

  • Chain '4':
    No sequence available.

  • Chain '5':
    No sequence available.

  • Chain '6':
    Sequence, based on SEQRES records: (download)
    >3d5b6 (6:)
    masevriklllecteckrrnyateknkrntpnklelrkycpwcrkhtvhrevki
    

    Sequence, based on observed residues (ATOM records): (download)
    >3d5b6 (6:)
    lllecteckrrnyateknkrntpnklelrkycpwcrkhtvhrev
    

  • Chain '7':
    Sequence, based on SEQRES records: (download)
    >3d5b7 (7:)
    mkrtwqpnrrkrakthgfrarmrtpggrkvlkrrrqkgrwrltpavrkr
    

    Sequence, based on observed residues (ATOM records): (download)
    >3d5b7 (7:)
    mkrtwqpnrrkrakthgfrarmrtpggrkvlkrrrqkgrwrltpavrk
    

  • Chain '8':
    No sequence available.

  • Chain 'A':
    No sequence available.

  • Chain 'B':
    No sequence available.

  • Chain 'D':
    No sequence available.

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >3d5bE (E:)
    mkgilgvkvgmtrifrddravpvtvilagpcpvvqrrtpekdgytavqlgflpqnpkrvn
    rplkghfakagvepvrilreirdfnpegdtvtveifkpgervdvtgtskgrgfagvmkrw
    nfaggpdshgahkihrhpgsignrktpgrvykgkkmaghygaervtvmnlevvdvipeen
    lllvkgavpgpngglvivretkkaak
    

    Sequence, based on observed residues (ATOM records): (download)
    >3d5bE (E:)
    mkgilgvkvgmtrifrddravpvtvilagpcpvvqrrtpekdgytavqlgflpqnpkrvn
    rplkghfakagvepvrilreirdfnpegdtvtveifkpgervdvtgtskgrgfagvmkrw
    nfaggpdshgahkihrhpgsignrktpgrvykgkkmaghygaervtvmnlevvdvipeen
    lllvkgavpgpngglvivretkka
    

  • Chain 'F':
    No sequence available.

  • Chain 'G':
    No sequence available.

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >3d5bH (H:)
    msrigrlpipvpkgvsvevapgrvkvkgpkgelevpvspemrvvveegvvrverpsderr
    hkslhgltrtlianavkgvsegyskellikgigyrarlvgraleltvgfshpvvveppeg
    itfevpeptrvrvsgidkqkvgqvaanirairkpsayhekgiyyagepvrlkpgkagakk
    

    Sequence, based on observed residues (ATOM records): (download)
    >3d5bH (H:)
    pkgvsvevapgrvkvkgpkgelevpvspemrvvveegvvrverpsderrhkslhgltrtl
    ianavkgvsegyskellikgigyrarlvgraleltvgfshpvvveppegitfevpeptrv
    rvsgidkqkvgqvaanirairkpsayhekgiyyagepvr
    

  • Chain 'I':
    No sequence available.

  • Chain 'J':
    No sequence available.

  • Chain 'N':
    Sequence, based on SEQRES records: (download)
    >3d5bN (N:)
    mvksslaflrgppiprqeqrralvktyvpkqveprwvlidaegktlgrlatkiatllrgk
    hrpdwtpnvamgdfvvvvnadkirvtgkkleqkiytrysgypgglkkiplekmlathper
    vlehavkgmlpkgplgrrlfkrlkvyagpdhphqaqrpeklev
    

    Sequence, based on observed residues (ATOM records): (download)
    >3d5bN (N:)
    ktyvpkqveprwvlidaegktlgrlatkiatllrgkhrpdwtpnvamgdfvvvvnadkir
    vtgkkleqkiytrysgypgglkkiplekmlathpervlehavkgmlpkgplgrrlfkrlk
    vyagpdhphqaqrpekl
    

  • Chain 'O':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3d5bO (O:)
    miqpqtylevadntgarkimcirvlkgsnakyatvgdvivasvkeaiprgavkegdvvka
    vvvrtkkevkrpdgsairfddnaaviinnqleprgtrvfgpvarelrekgfmkivslape
    vl
    

  • Chain 'P':
    Sequence, based on SEQRES records: (download)
    >3d5bP (P:)
    mklsdlrpnpgankrrkrvgrgpgsghgktatrghkgqksrsgglkdprrfeggrsttlm
    rlpkrgmqgqvpgeikrpryqgvnlkdlarfegevtpellvragllkkgyrlkilgegea
    kplkvvahafsksaleklkaaggepvllea
    

    Sequence, based on observed residues (ATOM records): (download)
    >3d5bP (P:)
    dlrpnpgankrrkrvgrgpgsghgktatrghkgqksrsgglkdprrfeggrsttlmrlpk
    rgmqgqvpgeikrpryqgvnlkdlarfegevtpellvragllkkgyrlkilgegeakplk
    vvahafsksaleklkaaggepvllea
    

  • Chain 'Q':
    No sequence available.

  • Chain 'R':
    No sequence available.

  • Chain 'S':
    No sequence available.

  • Chain 'T':
    No sequence available.

  • Chain 'U':
    Sequence, based on SEQRES records: (download)
    >3d5bU (U:)
    mpraktgvvrrrkhkkilklakgywglrsksfrkaretlfaagnyayahrkrrkrdfrrl
    wivrinaacrqhglnystfihglkkagievdrknladlavrepqvfaelverakaaqg
    

    Sequence, based on observed residues (ATOM records): (download)
    >3d5bU (U:)
    praktgvvrrrkhkkilklakgywglrsksfrkaretlfaagnyayahrkrrkrdfrrlw
    ivrinaacrqhglnystfihglkkagievdrknladlavrepqvfaelverakaaqg
    

  • Chain 'V':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3d5bV (V:)
    mfaivktggkqyrvepglklrvekldaepgatvelpvlllggektvvgtpvvegasvvae
    vlghgrgkkilvskfkakvqyrrkkghrqpytellikeirg
    

  • Chain 'W':
    No sequence available.

  • Chain 'X':
    No sequence available.

  • Chain 'Y':
    Sequence, based on SEQRES records: (download)
    >3d5bY (Y:)
    mrvkmhvkkgdtvlvasgkykgrvgkvkevlpkkyavivegvnivkkavrvspkypqggf
    iekeaplhaskvrpicpacgkptrvrkkflengkkirvcakcggaldtee
    

    Sequence, based on observed residues (ATOM records): (download)
    >3d5bY (Y:)
    rvkmhvkkgdtvlvasgkykgrvgkvkevlpkkyavivegvnivkkavrvspkypqggfi
    ekeaplhaskvrpicpacgkptrvrkkflengkkirvcak
    

  • Chain 'Z':
    Sequence, based on SEQRES records: (download)
    >3d5bZ (Z:)
    meyrlkayyregekpsalrragklpgvmynrhlnrkvyvdlvefdkvfrqasihhvivle
    lpdgqslptlvrqvnldkrrrrpehvdffvlsdepvemyvplrfvgtpagvraggvlqei
    hrdilvkvsprnipefievdvsgleigdslhasdlklppgvelavspeetiaavvppedv
    eklaeeaaaevaepevikkgkeeeee
    

    Sequence, based on observed residues (ATOM records): (download)
    >3d5bZ (Z:)
    yrlkayyregekpsalrragklpgvmynrhlnrkvyvdlvefdkvfrqasihhvivlelp
    dgqslptlvrqvnldkrrrrpehvdffvlsdepvemyvplrfvgtpagvraggvlqeihr
    dilvkvsprnipefievdvsgleigdslhasdlklppgvelavspeetiaavvppedvek
    laeeaaae