PDB entry 3df4

View 3df4 on RCSB PDB site
Description: Crystal structure of the bacterial ribosome from Escherichia coli in complex with hygromycin B. This file contains the 50S subunit of the second 70S ribosome. The entire crystal structure contains two 70S ribosomes.
Class: ribosome
Keywords: RNA-protein complex, RIBOSOME
Deposited on 2008-06-11, released 2008-08-19
The last revision prior to the SCOPe 2.02 freeze date was dated 2009-11-03, with a file datestamp of 2009-10-30.
Experiment type: XRAY
Resolution: 3.5 Å
R-factor: 0.269
AEROSPACI score: 0.03 (click here for full SPACI score report)

Chains and heterogens:

  • Chain '0':
    Compound: 50S ribosomal protein L32
    Species: Escherichia coli [TaxId:562]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df401
  • Chain '1':
    Compound: 50S ribosomal protein L33
    Species: Escherichia coli [TaxId:562]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df411
  • Chain '2':
    Compound: 50S ribosomal protein L34
    Species: Escherichia coli [TaxId:562]
    Gene:
    Database cross-references and differences (RAF-indexed):
  • Chain '3':
    Compound: 50S ribosomal protein L35
    Species: Escherichia coli [TaxId:562]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df431
  • Chain '4':
    Compound: 50S ribosomal protein L36
    Species: Escherichia coli [TaxId:562]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df441
  • Chain 'A':
    Compound: 5S ribosomal RNA
    Species: Escherichia coli [TaxId:562]
    Gene:
  • Chain 'B':
    Compound: 23S ribosomal RNA
    Species: Escherichia coli [TaxId:562]
    Gene:
  • Chain 'C':
    Compound: 50S ribosomal protein L2
    Species: Escherichia coli [TaxId:562]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df4c1, d3df4c2
  • Chain 'D':
    Compound: 50S ribosomal protein L3
    Species: Escherichia coli [TaxId:562]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df4d1
  • Chain 'E':
    Compound: 50S ribosomal protein L4
    Species: Escherichia coli [TaxId:562]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df4e1
  • Chain 'F':
    Compound: 50S ribosomal protein L5
    Species: Escherichia coli [TaxId:562]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df4f1
  • Chain 'G':
    Compound: 50S ribosomal protein L6
    Species: Escherichia coli [TaxId:562]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df4g1, d3df4g2
  • Chain 'H':
    Compound: 50S ribosomal protein L9
    Species: Escherichia coli [TaxId:562]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df4h1, d3df4h2
  • Chain 'I':
    Compound: 50S ribosomal protein L11
    Species: Escherichia coli [TaxId:562]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df4i1, d3df4i2
  • Chain 'J':
    Compound: 50S ribosomal protein L13
    Species: Escherichia coli [TaxId:562]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df4j1
  • Chain 'K':
    Compound: 50S ribosomal protein L14
    Species: Escherichia coli [TaxId:562]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df4k1
  • Chain 'L':
    Compound: 50S ribosomal protein L15
    Species: Escherichia coli [TaxId:562]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df4l1
  • Chain 'M':
    Compound: 50S ribosomal protein L16
    Species: Escherichia coli [TaxId:562]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df4m1
  • Chain 'N':
    Compound: 50S ribosomal protein L17
    Species: Escherichia coli [TaxId:562]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df4n1
  • Chain 'O':
    Compound: 50S ribosomal protein L18
    Species: Escherichia coli [TaxId:562]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df4o1
  • Chain 'P':
    Compound: 50S ribosomal protein L19
    Species: Escherichia coli [TaxId:562]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df4p1
  • Chain 'Q':
    Compound: 50S ribosomal protein L20
    Species: Escherichia coli [TaxId:562]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df4q1
  • Chain 'R':
    Compound: 50S ribosomal protein L21
    Species: Escherichia coli [TaxId:562]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df4r1
  • Chain 'S':
    Compound: 50S ribosomal protein L22
    Species: Escherichia coli [TaxId:562]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df4s1
  • Chain 'T':
    Compound: 50S ribosomal protein L23
    Species: Escherichia coli [TaxId:562]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df4t1
  • Chain 'U':
    Compound: 50S ribosomal protein L24
    Species: Escherichia coli [TaxId:562]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df4u1
  • Chain 'V':
    Compound: 50S ribosomal protein L25
    Species: Escherichia coli [TaxId:562]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df4v1
  • Chain 'W':
    Compound: 50S ribosomal protein L27
    Species: Escherichia coli [TaxId:562]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df4w1
  • Chain 'X':
    Compound: 50S ribosomal protein L29
    Species: Escherichia coli [TaxId:562]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df4x1
  • Chain 'Y':
    Compound: 50S ribosomal protein L30
    Species: Escherichia coli [TaxId:562]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df4y1
  • Chain 'Z':
    Compound: 50S ribosomal protein L28
    Species: Escherichia coli [TaxId:562]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df4z1
  • Heterogens: MG, ZN, HOH

PDB Chain Sequences:

  • Chain '0':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3df40 (0:)
    avqqnkptrskrgmrrshdaltavtslsvdktsgekhlrhhitadgyyrgrkviak
    

  • Chain '1':
    Sequence, based on SEQRES records: (download)
    >3df41 (1:)
    akgirekiklvssagtghfytttknkrtkpeklelkkfdpvvrqhviykeakik
    

    Sequence, based on observed residues (ATOM records): (download)
    >3df41 (1:)
    girekiklvssagtghfytttknkrtkpeklelkkfdpvvrqhviykeak
    

  • Chain '2':
    No sequence available.

  • Chain '3':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3df43 (3:)
    pkiktvrgaakrfkktgkggfkhkhanlrhiltkkatkrkrhlrpkamvskgdlglviac
    lpya
    

  • Chain '4':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3df44 (4:)
    mkvrasvkklcrnckivkrdgvirvicsaepkhkqrqg
    

  • Chain 'A':
    No sequence available.

  • Chain 'B':
    No sequence available.

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >3df4C (C:)
    mavvkckptspgrrhvvkvvnpelhkgkpfaplleknsksggrnnngrittrhiggghkq
    ayrivdfkrnkdgipavverleydpnrsanialvlykdgerryilapkglkagdqiqsgv
    daaikpgntlpmrnipvgstvhnvemkpgkggqlarsagtyvqivardgayvtlrlrsge
    mrkveadcratlgevgnaehmlrvlgkagaarwrgvrptvrgtamnpvdhphgggegrnf
    gkhpvtpwgvqtkgkktrsnkrtdkfivrrrsk
    

    Sequence, based on observed residues (ATOM records): (download)
    >3df4C (C:)
    avvkckptspgrrhvvkvvnpelhkgkpfaplleknsksggrnnngrittrhiggghkqa
    yrivdfkrnkdgipavverleydpnrsanialvlykdgerryilapkglkagdqiqsgvd
    aaikpgntlpmrnipvgstvhnvemkpgkggqlarsagtyvqivardgayvtlrlrsgem
    rkveadcratlgevgnaehmlrvlgkagaarwrgvrptvrgtamnpvdhphgggegrnfg
    khpvtpwgvqtkgkktrsnkrtdkfivrrrs
    

  • Chain 'D':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3df4D (D:)
    miglvgkkvgmtriftedgvsipvtvieveanrvtqvkdlandgyraiqvttgakkanrv
    tkpeaghfakagveagrglwefrlaegeeftvgqsisvelfadvkkvdvtgtskgkgfag
    tvkrwnfrtqdathgnslshrvpgsigqnqtpgkvfkgkkmagqmgnervtvqsldvvrv
    daernlllvkgavpgatgsdlivkpavka
    

  • Chain 'E':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3df4E (E:)
    melvlkdaqsaltvsettfgrdfnealvhqvvvayaagarqgtraqktraevtgsgkkpw
    rqkgtgrarsgsikspiwrsggvtfaarpqdhsqkvnkkmyrgalksilselvrqdrliv
    vekfsveapktkllaqklkdmaledvliitgeldenlflaarnlhkvdvrdatgidpvsl
    iafdkvvmtadavkqveemla
    

  • Chain 'F':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3df4F (F:)
    aklhdyykdevvkklmtefnynsvmqvprvekitlnmgvgeaiadkklldnaaadlaais
    gqkplitkarksvagfkirqgypigckvtlrgermwefferlitiavprirdfrglsaks
    fdgrgnysmgvreqiifpeidydkvdrvrgldititttaksdeegrallaafdfpfrk
    

  • Chain 'G':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3df4G (G:)
    srvakapvvvpagvdvkingqvitikgkngeltrtlndavevkhadntltfgprdgyadg
    waqagtarallnsmvigvtegftkklqlvgvgyraavkgnvinlslgfshpvdhqlpagi
    taecptqteivlkgadkqvigqvaadlrayrrpepykgkgvryadevvrtkeakkk
    

  • Chain 'H':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3df4H (H:)
    mqvilldkvanlgslgdqvnvkagyarnflvpqgkavpatkknieffearraeleaklae
    vlaaanaraekinaletvtiaskagdegklfgsigtrdiadavtaagvevaksevrlpng
    vlrttgehevsfqvhsevfakvivnvvae
    

  • Chain 'I':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3df4I (I:)
    akkvqayvklqvaagmanpsppvgpalgqqgvnimefckafnaktdsiekglpipvvitv
    yadrsftfvtktppaavllkkaagiksgsgkpnkdkvgkisraqlqeiaqtkaadmtgad
    ieamtrsiegtarsmglvved
    

  • Chain 'J':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3df4J (J:)
    mktftakpetvkrdwyvvdatgktlgrlatelarrlrgkhkaeytphvdtgdyiivlnad
    kvavtgnkrtdkvyyhhtghiggikqatfeemiarrpervieiavkgmlpkgplgramfr
    klkvyagnehnhaaqqpqvldi
    

  • Chain 'K':
    Sequence, based on SEQRES records: (download)
    >3df4K (K:)
    miqeqtmlnvadnsgarrvmcikvlggshrryagvgdiikitikeaiprgkvkkgdvlka
    vvvrtkkgvrrpdgsvirfdgnacvllnnnseqpigtrifgpvtrelrsekfmkiislap
    evl
    

    Sequence, based on observed residues (ATOM records): (download)
    >3df4K (K:)
    iqeqtmlnvadnsgarrvmcikvlggshrryagvgdiikitikeaiprgkvkkgdvlkav
    vvrtkkgvrrpdgsvirfdgnacvllnnnseqpigtrifgpvtrelrsekfmkiislape
    v
    

  • Chain 'L':
    Sequence, based on SEQRES records: (download)
    >3df4L (L:)
    mrlntlspaegskkagkrlgrgigsglgktggrghkgqksrsgggvrrgfeggqmplyrr
    lpkfgftsrkaaitaeirlsdlakveggvvdlntlkaaniigiqiefakvilagevttpv
    tvrglrvtkgaraaieaaggkiee
    

    Sequence, based on observed residues (ATOM records): (download)
    >3df4L (L:)
    rlntlspaegskkagkrlgrgigsglgktggrghkgqksrsgggvrrgfeggqmplyrrl
    pkfgftsrkaaitaeirlsdlakveggvvdlntlkaaniigiqiefakvilagevttpvt
    vrglrvtkgaraaieaaggkiee
    

  • Chain 'M':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3df4M (M:)
    mlqpkrtkfrkmhkgrnrglaqgtdvsfgsfglkavgrgrltarqieaarramtravkrq
    gkiwirvfpdkpitekplavrmgkgkgnveywvaliqpgkvlyemdgvpeelareafkla
    aaklpikttfvtktvm
    

  • Chain 'N':
    Sequence, based on SEQRES records: (download)
    >3df4N (N:)
    mrhrksgrqlnrnsshrqamfrnmagslvrheiikttlpkakelrrvveplitlaktdsv
    anrrlafartrdneivaklfnelgprfasraggytrilkcgfragdnapmayielvdrse
    kaeaaae
    

    Sequence, based on observed residues (ATOM records): (download)
    >3df4N (N:)
    mrhrksgrqlnrnsshrqamfrnmagslvrheiikttlpkakelrrvveplitlaktdsv
    anrrlafartrdneivaklfnelgprfasraggytrilkcgfragdnapmayielvdrse
    

  • Chain 'O':
    Sequence, based on SEQRES records: (download)
    >3df4O (O:)
    mdkksarirratrarrklqelgatrlvvhrtprhiyaqviapngsevlvaastvekaiae
    qlkytgnkdaaaavgkavaeralekgikdvsfdrsgfqyhgrvqaladaareaglqf
    

    Sequence, based on observed residues (ATOM records): (download)
    >3df4O (O:)
    dkksarirratrarrklqelgatrlvvhrtprhiyaqviapngsevlvaastvekaiaeq
    lkytgnkdaaaavgkavaeralekgikdvsfdrsgfqyhgrvqaladaareaglqf
    

  • Chain 'P':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3df4P (P:)
    sniikqleqeqmkqdvpsfrpgdtvevkvwvvegskkrlqafegvviairnrglhsaftv
    rkisngegvervfqthspvvdsisvkrrgavrkaklyylrertgkaarikerln
    

  • Chain 'Q':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3df4Q (Q:)
    arvkrgviararhkkilkqakgyygarsrvyrvafqavikagqyayrdrrqrkrqfrqlw
    iarinaaarqngisyskfinglkkasveidrkiladiavfdkvaftalvekakaala
    

  • Chain 'R':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3df4R (R:)
    myavfqsggkqhrvsegqtvrlekldiatgetvefaevlmiangeevkigvpfvdggvik
    aevvahgrgekvkivkfrrrkhyrkqqghrqwftdvkitgisa
    

  • Chain 'S':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3df4S (S:)
    metiakhrharssaqkvrlvadlirgkkvsqaldiltytnkkaavlvkkvlesaianaeh
    ndgadiddlkvtkifvdegpsmkrimprakgradrilkrtshitvvvsdr
    

  • Chain 'T':
    Sequence, based on SEQRES records: (download)
    >3df4T (T:)
    mireerllkvlraphvsekastameksntivlkvakdatkaeikaavqklfevevevvnt
    lvvkgkvkrhgqrigrrsdwkkayvtlkegqnldfvggae
    

    Sequence, based on observed residues (ATOM records): (download)
    >3df4T (T:)
    mireerllkvlraphvsekastameksntivlkvakdatkaeikaavqklfevevevvnt
    lvvkgkvkrhgqrigrrsdwkkayvtlkegqnl
    

  • Chain 'U':
    Sequence, based on SEQRES records: (download)
    >3df4U (U:)
    aakirrddevivltgkdkgkrgkvknvlssgkviveginlvkkhqkpvpalnqpggivek
    eaaiqvsnvaifnaatgkadrvgfrfedgkkvrffksnsetik
    

    Sequence, based on observed residues (ATOM records): (download)
    >3df4U (U:)
    aakirrddevivltgkdkgkrgkvknvlssgkviveginlvkkhqkpvpalnqpggivek
    eaaiqvsnvaifnaatgkadrvgfrfedgkkvrffksnseti
    

  • Chain 'V':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3df4V (V:)
    mftinaevrkeqgkgasrrlraankfpaiiyggkeaplaieldhdkvmnmqakaefysev
    ltivvdgkeikvkaqdvqrhpykpklqhidfvra
    

  • Chain 'W':
    Sequence, based on SEQRES records: (download)
    >3df4W (W:)
    ahkkaggstrngrdseakrlgvkrfggesvlagsiivrqrgtkfhaganvgcgrdhtlfa
    kadgkvkfevkgpknrkfisieae
    

    Sequence, based on observed residues (ATOM records): (download)
    >3df4W (W:)
    ggstrngrdseakrlgvkrfggesvlagsiivrqrgtkfhaganvgcgrdhtlfakadgk
    vkfevkgpknrkfisieae
    

  • Chain 'X':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3df4X (X:)
    mkakelreksveelntellnllreqfnlrmqaasgqlqqshllkqvrrdvarvktllnek
    aga
    

  • Chain 'Y':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3df4Y (Y:)
    aktikitqtrsaigrlpkhkatllglglrrightveredtpairgminavsfmvkvee
    

  • Chain 'Z':
    Sequence, based on SEQRES records: (download)
    >3df4Z (Z:)
    msrvcqvtgkrpvtgnnrshalnatkrrflpnlhshrfwvesekrfvtlrvsakgmrvid
    kkgidtvlaelrargeky
    

    Sequence, based on observed residues (ATOM records): (download)
    >3df4Z (Z:)
    srvcqvtgkrpvtgnnrshalnatkrrflpnlhshrfwvesekrfvtlrvsakgmrvidk
    kgidtvlaelrargeky