PDB entry 2vhm

View 2vhm on RCSB PDB site
Description: structure of pdf binding helix in complex with the ribosome (part 1 of 4)
Class: ribosome
Keywords: translation, peptide deformylase, RNA-protein complex, ribosomal protein, ribonucleoprotein, 50s ribosomal subunit, antibiotic resistance, ribosome, nascent chain processing, RNA-binding, translation regulation, tRNA binding, protein biosynthesis
Deposited on 2007-11-22, released 2008-02-26
The last revision prior to the SCOPe 2.01 freeze date was dated 2009-02-24, with a file datestamp of 2009-03-01.
Experiment type: XRAY
Resolution: 3.74 Å
R-factor: 0.259
AEROSPACI score: -0.01 (click here for full SPACI score report)

Chains and heterogens:

  • Chain '0':
    Compound: 50S ribosomal protein L32
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d2vhm01
  • Chain '1':
    Compound: 50S ribosomal protein L33
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d2vhm11
  • Chain '2':
    Compound: 50S ribosomal protein L34
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed):
  • Chain '3':
    Compound: 50S ribosomal protein L35
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d2vhm31
  • Chain '4':
    Compound: 50S ribosomal protein L36
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d2vhm41
  • Chain '5':
    Compound: c-term helix pdf
    Species: Escherichia coli, synthetic [TaxId:562]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P0A6K3 (0-15)
      • engineered mutation (0)
  • Chain 'A':
    Compound: 5S ribosomal RNA
    Species: Escherichia coli [TaxId:562]
  • Chain 'B':
    Compound: 23S ribosomal RNA
    Species: Escherichia coli [TaxId:562]
  • Chain 'C':
    Compound: 50S ribosomal protein L2
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d2vhmc1, d2vhmc2
  • Chain 'D':
    Compound: 50S ribosomal protein L3
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d2vhmd1
  • Chain 'E':
    Compound: 50S ribosomal protein L4
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d2vhme1
  • Chain 'F':
    Compound: 50S ribosomal protein L5
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d2vhmf1
  • Chain 'G':
    Compound: 50S ribosomal protein L6
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d2vhmg1, d2vhmg2
  • Chain 'H':
    Compound: 50S ribosomal protein L9
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d2vhmh1, d2vhmh2
  • Chain 'I':
    Compound: 50S ribosomal protein L11
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d2vhmi1, d2vhmi2
  • Chain 'J':
    Compound: 50S ribosomal protein L13
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d2vhmj1
  • Chain 'K':
    Compound: 50S ribosomal protein L14
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d2vhmk1
  • Chain 'L':
    Compound: 50S ribosomal protein L15
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d2vhml1
  • Chain 'M':
    Compound: 50S ribosomal protein L16
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d2vhmm1
  • Chain 'N':
    Compound: 50S ribosomal protein L17
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d2vhmn1
  • Chain 'O':
    Compound: 50S ribosomal protein L18
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d2vhmo1
  • Chain 'P':
    Compound: 50S ribosomal protein L19
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d2vhmp1
  • Chain 'Q':
    Compound: 50S ribosomal protein L20
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d2vhmq1
  • Chain 'R':
    Compound: 50S ribosomal protein L21
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d2vhmr1
  • Chain 'S':
    Compound: 50S ribosomal protein L22
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d2vhms1
  • Chain 'T':
    Compound: 50S ribosomal protein L23
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d2vhmt1
  • Chain 'U':
    Compound: 50S ribosomal protein L24
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d2vhmu1
  • Chain 'V':
    Compound: 50S ribosomal protein L25
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d2vhmv1
  • Chain 'W':
    Compound: 50S ribosomal protein L27
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d2vhmw1
  • Chain 'X':
    Compound: 50S ribosomal protein L29
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d2vhmx1
  • Chain 'Y':
    Compound: 50S ribosomal protein L30
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d2vhmy1
  • Chain 'Z':
    Compound: 50S ribosomal protein L31
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d2vhmz1
  • Heterogens: MG, HOH

PDB Chain Sequences:

  • Chain '0':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2vhm0 (0:)
    avqqnkptrskrgmrrshdaltavtslsvdktsgekhlrhhitadgyyrgrkviak
    

  • Chain '1':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2vhm1 (1:)
    akgirekiklvssagtghfytttknkrtkpeklelkkfdpvvrqhviykeakik
    

  • Chain '2':
    No sequence available.

  • Chain '3':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2vhm3 (3:)
    pkiktvrgaakrfkktgkggfkhkhanlrhiltkkatkrkrhlrpkamvskgdlglviac
    lpya
    

  • Chain '4':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2vhm4 (4:)
    mkvrasvkklcrnckivkrdgvirvicsaepkhkqrqg
    

  • Chain '5':
    No sequence available.

  • Chain 'A':
    No sequence available.

  • Chain 'B':
    No sequence available.

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >2vhmC (C:)
    mavvkckptspgrrhvvkvvnpelhkgkpfaplleknsksggrnnngrittrhiggghkq
    ayrivdfkrnkdgipavverleydpnrsanialvlykdgerryilapkglkagdqiqsgv
    daaikpgntlpmrnipvgstvhnvemkpgkggqlarsagtyvqivardgayvtlrlrsge
    mrkveadcratlgevgnaehmlrvlgkagaarwrgvrptvrgtamnpvdhphgggegrnf
    gkhpvtpwgvqtkgkktrsnkrtdkfivrrrsk
    

    Sequence, based on observed residues (ATOM records): (download)
    >2vhmC (C:)
    vkckptspgrrhvvkvvnpelhkgkpfaplleknsksggrnnngrittrhiggghkqayr
    ivdfkrnkdgipavverleydpnrsanialvlykdgerryilapkglkagdqiqsgvdaa
    ikpgntlpmrnipvgstvhnvemkpgkggqlarsagtyvqivardgayvtlrlrsgemrk
    veadcratlgevgnaehmlrvlgkagaarwrgvrptvrgtamnpvdhphgggegrnfgkh
    pvtpwgvqtkgkktrsnkrtdkfivrrr
    

  • Chain 'D':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2vhmD (D:)
    miglvgkkvgmtriftedgvsipvtvieveanrvtqvkdlandgyraiqvttgakkanrv
    tkpeaghfakagveagrglwefrlaegeeftvgqsisvelfadvkkvdvtgtskgkgfag
    tvkrwnfrtqdathgnslshrvpgsigqnqtpgkvfkgkkmagqmgnervtvqsldvvrv
    daernlllvkgavpgatgsdlivkpavka
    

  • Chain 'E':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2vhmE (E:)
    melvlkdaqsaltvsettfgrdfnealvhqvvvayaagarqgtraqktraevtgsgkkpw
    rqkgtgrarsgsikspiwrsggvtfaarpqdhsqkvnkkmyrgalksilselvrqdrliv
    vekfsveapktkllaqklkdmaledvliitgeldenlflaarnlhkvdvrdatgidpvsl
    iafdkvvmtadavkqveemla
    

  • Chain 'F':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2vhmF (F:)
    aklhdyykdevvkklmtefnynsvmqvprvekitlnmgvgeaiadkklldnaaadlaais
    gqkplitkarksvagfkirqgypigckvtlrgermwefferlitiavprirdfrglsaks
    fdgrgnysmgvreqiifpeidydkvdrvrgldititttaksdeegrallaafdfpfrk
    

  • Chain 'G':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2vhmG (G:)
    srvakapvvvpagvdvkingqvitikgkngeltrtlndavevkhadntltfgprdgyadg
    waqagtarallnsmvigvtegftkklqlvgvgyraavkgnvinlslgfshpvdhqlpagi
    taecptqteivlkgadkqvigqvaadlrayrrpepykgkgvryadevvrtkeakkk
    

  • Chain 'H':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2vhmH (H:)
    mqvilldkvanlgslgdqvnvkagyarnflvpqgkavpatkknieffearraeleaklae
    vlaaanaraekinaletvtiaskagdegklfgsigtrdiadavtaagvevaksevrlpng
    vlrttgehevsfqvhsevfakvivnvvae
    

  • Chain 'I':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2vhmI (I:)
    akkvqayvklqvaagmanpsppvgpalgqqgvnimefckafnaktdsiekglpipvvitv
    yadrsftfvtktppaavllkkaagiksgsgkpnkdkvgkisraqlqeiaqtkaadmtgad
    ieamtrsiegtarsmglvved
    

  • Chain 'J':
    Sequence, based on SEQRES records: (download)
    >2vhmJ (J:)
    mktftakpetvkrdwyvvdatgktlgrlatelarrlrgkhkaeytphvdtgdyiivlnad
    kvavtgnkrtdkvyyhhtghiggikqatfeemiarrpervieiavkgmlpkgplgramfr
    klkvyagnehnhaaqqpqvldi
    

    Sequence, based on observed residues (ATOM records): (download)
    >2vhmJ (J:)
    mktftakpetvkrdwyvvdatgktlgrlatelarrlrgkhkaeytphvdtgdyiivlnad
    kvavtgnkrtdkvyyhhtghiggikqatfeemiarrpervieiavkgmlpkgplgramfr
    klkvyagnehnhaaqqpqvld
    

  • Chain 'K':
    Sequence, based on SEQRES records: (download)
    >2vhmK (K:)
    miqeqtmlnvadnsgarrvmcikvlggshrryagvgdiikitikeaiprgkvkkgdvlka
    vvvrtkkgvrrpdgsvirfdgnacvllnnnseqpigtrifgpvtrelrsekfmkiislap
    evl
    

    Sequence, based on observed residues (ATOM records): (download)
    >2vhmK (K:)
    iqeqtmlnvadnsgarrvmcikvlggshrryagvgdiikitikeaiprgkvkkgdvlkav
    vvrtkkgvrrpdgsvirfdgnacvllnnnseqpigtrifgpvtrelrsekfmkiislape
    vl
    

  • Chain 'L':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2vhmL (L:)
    mrlntlspaegskkagkrlgrgigsglgktggrghkgqksrsgggvrrgfeggqmplyrr
    lpkfgftsrkaaitaeirlsdlakveggvvdlntlkaaniigiqiefakvilagevttpv
    tvrglrvtkgaraaieaaggkiee
    

  • Chain 'M':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2vhmM (M:)
    mlqpkrtkfrkmhkgrnrglaqgtdvsfgsfglkavgrgrltarqieaarramtravkrq
    gkiwirvfpdkpitekplavrmgkgkgnveywvaliqpgkvlyemdgvpeelareafkla
    aaklpikttfvtktvm
    

  • Chain 'N':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2vhmN (N:)
    mrhrksgrqlnrnsshrqamfrnmagslvrheiikttlpkakelrrvveplitlaktdsv
    anrrlafartrdneivaklfnelgprfasraggytrilkcgfragdnapmayielvdrse
    kaeaaae
    

  • Chain 'O':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2vhmO (O:)
    mdkksarirratrarrklqelgatrlvvhrtprhiyaqviapngsevlvaastvekaiae
    qlkytgnkdaaaavgkavaeralekgikdvsfdrsgfqyhgrvqaladaareaglqf
    

  • Chain 'P':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2vhmP (P:)
    sniikqleqeqmkqdvpsfrpgdtvevkvwvvegskkrlqafegvviairnrglhsaftv
    rkisngegvervfqthspvvdsisvkrrgavrkaklyylrertgkaarikerln
    

  • Chain 'Q':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2vhmQ (Q:)
    arvkrgviararhkkilkqakgyygarsrvyrvafqavikagqyayrdrrqrkrqfrqlw
    iarinaaarqngisyskfinglkkasveidrkiladiavfdkvaftalvekakaala
    

  • Chain 'R':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2vhmR (R:)
    myavfqsggkqhrvsegqtvrlekldiatgetvefaevlmiangeevkigvpfvdggvik
    aevvahgrgekvkivkfrrrkhyrkqqghrqwftdvkitgisa
    

  • Chain 'S':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2vhmS (S:)
    metiakhrharssaqkvrlvadlirgkkvsqaldiltytnkkaavlvkkvlesaianaeh
    ndgadiddlkvtkifvdegpsmkrimprakgradrilkrtshitvvvsdr
    

  • Chain 'T':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2vhmT (T:)
    mireerllkvlraphvsekastameksntivlkvakdatkaeikaavqklfevevevvnt
    lvvkgkvkrhgqrigrrsdwkkayvtlkegqnldfvggae
    

  • Chain 'U':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2vhmU (U:)
    aakirrddevivltgkdkgkrgkvknvlssgkviveginlvkkhqkpvpalnqpggivek
    eaaiqvsnvaifnaatgkadrvgfrfedgkkvrffksnsetik
    

  • Chain 'V':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2vhmV (V:)
    mftinaevrkeqgkgasrrlraankfpaiiyggkeaplaieldhdkvmnmqakaefysev
    ltivvdgkeikvkaqdvqrhpykpklqhidfvra
    

  • Chain 'W':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2vhmW (W:)
    ahkkaggstrngrdseakrlgvkrfggesvlagsiivrqrgtkfhaganvgcgrdhtlfa
    kadgkvkfevkgpknrkfisieae
    

  • Chain 'X':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2vhmX (X:)
    mkakelreksveelntellnllreqfnlrmqaasgqlqqshllkqvrrdvarvktllnek
    aga
    

  • Chain 'Y':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2vhmY (Y:)
    aktikitqtrsaigrlpkhkatllglglrrightveredtpairgminavsfmvkvee
    

  • Chain 'Z':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2vhmZ (Z:)
    mkkdihpkyeeitascscgnvmkirstvghdlnldvcskchpfftgkqrdvatggrvdrf
    nkrfnipgsk