PDB entry 3df1

View 3df1 on RCSB PDB site
Description: Crystal structure of the bacterial ribosome from Escherichia coli in complex with hygromycin B. This file contains the 30S subunit of the first 70S ribosome, with hygromycin B bound. 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: 0.05 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: 16S ribosomal RNA
    Species: Escherichia coli [TaxId:562]
  • Chain 'B':
    Compound: 30S ribosomal protein S2
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df1b1
  • Chain 'C':
    Compound: 30S ribosomal protein S3
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df1c1, d3df1c2
  • Chain 'D':
    Compound: 30S ribosomal protein S4
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df1d1
  • Chain 'E':
    Compound: 30S ribosomal protein S5
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df1e1, d3df1e2
  • Chain 'F':
    Compound: 30S ribosomal protein S6
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df1f1
  • Chain 'G':
    Compound: 30S ribosomal protein S7
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df1g1
  • Chain 'H':
    Compound: 30S ribosomal protein S8
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df1h1
  • Chain 'I':
    Compound: 30S ribosomal protein S9
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df1i1
  • Chain 'J':
    Compound: 30S ribosomal protein S10
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df1j1
  • Chain 'K':
    Compound: 30S ribosomal protein S11
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df1k1
  • Chain 'L':
    Compound: 30S ribosomal protein S12
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df1l1
  • Chain 'M':
    Compound: 30S ribosomal protein S13
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df1m1
  • Chain 'N':
    Compound: 30S ribosomal protein S14
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df1n1
  • Chain 'O':
    Compound: 30S ribosomal protein S15
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df1o1
  • Chain 'P':
    Compound: 30S ribosomal protein S16
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df1p1
  • Chain 'Q':
    Compound: 30S ribosomal protein S17
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df1q1
  • Chain 'R':
    Compound: 30S ribosomal protein S18
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df1r1
  • Chain 'S':
    Compound: 30S ribosomal protein S19
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df1s1
  • Chain 'T':
    Compound: 30S ribosomal protein S20
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df1t1
  • Chain 'U':
    Compound: 30S ribosomal protein S21
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.02: d3df1u1
  • Heterogens: MG, HYG, HOH

PDB Chain Sequences:

  • Chain 'A':
    No sequence available.

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >3df1B (B:)
    atvsmrdmlkagvhfghqtrywnpkmkpfifgarnkvhiinlektvpmfnealaelnkia
    srkgkilfvgtkraaseavkdaalscdqffvnhrwlggmltnwktvrqsikrlkdletqs
    qdgtfdkltkkealmrtreleklenslggikdmgglpdalfvidadhehiaikeannlgi
    pvfaivdtnsdpdgvdfvipgnddairavtlylgavaatvregrsqdlasqaeesfveae
    

    Sequence, based on observed residues (ATOM records): (download)
    >3df1B (B:)
    mlkagvhfghqtrywnpkmkpfifgarnkvhiinlektvpmfnealaelnkiasrkgkil
    fvgtkraaseavkdaalscdqffvnhrwlggmltnwktvrqsikrlkdletqsqdgtfdk
    ltkkealmrtreleklenslggikdmgglpdalfvidadhehiaikeannlgipvfaivd
    tnsdpdgvdfvipgnddairavtlylgavaatvregrs
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >3df1C (C:)
    gqkvhpngirlgivkpwnstwfantkefadnldsdfkvrqyltkelakasvsrivierpa
    ksirvtihtarpgivigkkgedveklrkvvadiagvpaqiniaevrkpeldaklvadsit
    sqlerrvmfrramkravqnamrlgakgikvevsgrlggaeiartewyregrvplhtlrad
    idyntseahttygvigvkvwifkgeilggmaaveqpekpaaqpkkqqrkgrk
    

    Sequence, based on observed residues (ATOM records): (download)
    >3df1C (C:)
    gqkvhpngirlgivkpwnstwfantkefadnldsdfkvrqyltkelakasvsrivierpa
    ksirvtihtarpgivigkkgedveklrkvvadiagvpaqiniaevrkpeldaklvadsit
    sqlerrvmfrramkravqnamrlgakgikvevsgrlggaeiartewyregrvplhtlrad
    idyntseahttygvigvkvwifkgei
    

  • Chain 'D':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3df1D (D:)
    arylgpklklsrregtdlflksgvraidtkckieqapgqhgarkprlsdygvqlrekqkv
    rriygvlerqfrnyykeaarlkgntgenllallegrldnvvyrmgfgatraearqlvshk
    aimvngrvvniasyqvspndvvsirekakkqsrvkaalelaeqrekptwlevdagkmegt
    fkrkpersdlsadinehlivelysk
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >3df1E (E:)
    ahiekqagelqekliavnrvsktvkggrifsftaltvvgdgngrvgfgygkarevpaaiq
    kamekarrnminvalnngtlqhpvkgvhtgsrvfmqpasegtgiiaggamravlevagvh
    nvlakaygstnpinvvratidglenmnspemvaakrgksveeilgk
    

    Sequence, based on observed residues (ATOM records): (download)
    >3df1E (E:)
    elqekliavnrvsktvkggrifsftaltvvgdgngrvgfgygkarevpaaiqkamekarr
    nminvalnngtlqhpvkgvhtgsrvfmqpasegtgiiaggamravlevagvhnvlakayg
    stnpinvvratidglenmnspemvaakrgk
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >3df1F (F:)
    mrhyeivfmvhpdqseqvpgmierytaaitgaegkihrledwgrrqlaypinklhkahyv
    lmnveapqevidelettfrfndavirsmvmrtkhavteaspmvkakderrerrddfanet
    addaeagdseeeeee
    

    Sequence, based on observed residues (ATOM records): (download)
    >3df1F (F:)
    mrhyeivfmvhpdqseqvpgmierytaaitgaegkihrledwgrrqlaypinklhkahyv
    lmnveapqevidelettfrfndavirsmvmrtkhavteas
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >3df1G (G:)
    prrrvigqrkilpdpkfgsellakfvnilmvdgkkstaesivysaletlaqrsgkselea
    fevalenvrptvevksrrvggstyqvpvevrpvrrnalamrwiveaarkrgdksmalrla
    nelsdaaenkgtavkkredvhrmaeankafahyrwlslrsfshqagasskqpalgyln
    

    Sequence, based on observed residues (ATOM records): (download)
    >3df1G (G:)
    rrrvigqrkilpdpkfgsellakfvnilmvdgkkstaesivysaletlaqrsgkseleaf
    evalenvrptvevksrrvggstyqvpvevrpvrrnalamrwiveaarkrgdksmalrlan
    elsdaaenkgtavkkredvhrmaeankafa
    

  • Chain 'H':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3df1H (H:)
    smqdpiadmltrirngqaankaavtmpssklkvaianvlkeegfiedfkvegdtkpelel
    tlkyfqgkavvesiqrvsrpglriykrkdelpkvmaglgiavvstskgvmtdraarqagl
    ggeiicyva
    

  • Chain 'I':
    Sequence, based on SEQRES records: (download)
    >3df1I (I:)
    aenqyygtgrrkssaarvfikpgngkivinqrsleqyfgretarmvvrqplelvdmvekl
    dlyitvkgggisgqagairhgitralmeydeslrselrkagfvtrdarqverkkvglrka
    rrrpqfskr
    

    Sequence, based on observed residues (ATOM records): (download)
    >3df1I (I:)
    nqyygtgrrkssaarvfikpgngkivinqrsleqyfgretarmvvrqplelvdmvekldl
    yitvkgggisgqagairhgitralmeydeslrselrkagfvtrdarqverkkvglrkarr
    rpqfskr
    

  • Chain 'J':
    Sequence, based on SEQRES records: (download)
    >3df1J (J:)
    mqnqririrlkafdhrlidqataeivetakrtgaqvrgpiplptrkerftvlisphvnkd
    ardqyeirthlrlvdiveptektvdalmrldlaagvdvqislg
    

    Sequence, based on observed residues (ATOM records): (download)
    >3df1J (J:)
    ririrlkafdhrlidqataeivetakrtgaqvrgpiplptrkerftvlisphvnkdardq
    yeirthlrlvdiveptektvdalmrldlaagvdvqisl
    

  • Chain 'K':
    Sequence, based on SEQRES records: (download)
    >3df1K (K:)
    akapirarkrvrkqvsdgvahihasfnntivtitdrqgnalgwataggsgfrgsrkstpf
    aaqvaaercadavkeygiknlevmvkgpgpgrestiralnaagfritnitdvtpiphngc
    rppkkrrv
    

    Sequence, based on observed residues (ATOM records): (download)
    >3df1K (K:)
    rkqvsdgvahihasfnntivtitdrqgnalgwataggsgfrgsrkstpfaaqvaaercad
    avkeygiknlevmvkgpgpgrestiralnaagfritnitdvtpiphngcrppkkrrv
    

  • Chain 'L':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3df1L (L:)
    atvnqlvrkprarkvaksnvpaleacpqkrgvctrvytttpkkpnsalrkvcrvrltngf
    evtsyiggeghnlqehsvilirggrvkdlpgvryhtvrgaldcsgvkdrkqarskygvkr
    pka
    

  • Chain 'M':
    Sequence, based on SEQRES records: (download)
    >3df1M (M:)
    ariaginipdhkhavialtsiygvgktrskailaaagiaedvkiselsegqidtlrdeva
    kfvvegdlrreismsikrlmdlgcyrglrhrrglpvrgqrtktnartrkgprkpikk
    

    Sequence, based on observed residues (ATOM records): (download)
    >3df1M (M:)
    ariaginipdhkhavialtsiygvgktrskailaaagiaedvkiselsegqidtlrdeva
    kfvvegdlrreismsikrlmdlgcyrglrhrrglpvrgqrtktnartrkgprkp
    

  • Chain 'N':
    Sequence, based on SEQRES records: (download)
    >3df1N (N:)
    akqsmkarevkrvaladkyfakraelkaiisdvnasdedrwnavlklqtlprdsspsrqr
    nrcrqtgrphgflrkfglsrikvreaamrgeipglkkasw
    

    Sequence, based on observed residues (ATOM records): (download)
    >3df1N (N:)
    akqsmkarevkrvaladkyfakraelkaiisdvnarwnavlklqtlprdsspsrqrnrcr
    qtgrphgflrkfglsrikvreaamrgeipglkkasw
    

  • Chain 'O':
    Sequence, based on SEQRES records: (download)
    >3df1O (O:)
    mslsteatakivsefgrdandtgstevqvalltaqinhlqghfaehkkdhhsrrgllrmv
    sqrrklldylkrkdvarytrlierlglrr
    

    Sequence, based on observed residues (ATOM records): (download)
    >3df1O (O:)
    slsteatakivsefgrdandtgstevqvalltaqinhlqghfaehkkdhhsrrgllrmvs
    qrrklldylkrkdvarytrlierlglrr
    

  • Chain 'P':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3df1P (P:)
    mvtirlarhgakkrpfyqvvvadsrnarngrfiervgffnpiasekeegtrldldriahw
    vgqgatisdrvaalikevnkaa
    

  • Chain 'Q':
    Sequence, based on SEQRES records: (download)
    >3df1Q (Q:)
    tdkirtlqgrvvsdkmeksivvaierfvkhpiygkfikrttklhvhdennecgigdvvei
    recrplsktkswtlvrvvekavl
    

    Sequence, based on observed residues (ATOM records): (download)
    >3df1Q (Q:)
    kirtlqgrvvsdkmeksivvaierfvkhpiygkfikrttklhvhdennecgigdvveire
    crplsktkswtlvrvvekav
    

  • Chain 'R':
    Sequence, based on SEQRES records: (download)
    >3df1R (R:)
    aryfrrrkfcrftaegvqeidykdiatlknyitesgkivpsritgtrakyqrqlaraikr
    arylsllpytdrhq
    

    Sequence, based on observed residues (ATOM records): (download)
    >3df1R (R:)
    eidykdiatlknyitesgkivpsritgtrakyqrqlaraikrarylsllpytdrh
    

  • Chain 'S':
    Sequence, based on SEQRES records: (download)
    >3df1S (S:)
    prslkkgpfidlhllkkvekavesgdkkplrtwsrrstifpnmigltiavhngrqhvpvf
    vtdemvghklgefaptrtyrghaadkkakkk
    

    Sequence, based on observed residues (ATOM records): (download)
    >3df1S (S:)
    rslkkgpfidlhllkkvekavesgdkkplrtwsrrstifpnmigltiavhngrqhvpvfv
    tdemvghklgefaptrtyr
    

  • Chain 'T':
    Sequence, based on SEQRES records: (download)
    >3df1T (T:)
    aniksakkraiqsekarkhnasrrsmmrtfikkvyaaieagdkaaaqkafnemqpivdrq
    aakglihknkaarhkanltaqinkla
    

    Sequence, based on observed residues (ATOM records): (download)
    >3df1T (T:)
    niksakkraiqsekarkhnasrrsmmrtfikkvyaaieagdkaaaqkafnemqpivdrqa
    akglihknkaarhkanltaqinkla
    

  • Chain 'U':
    Sequence, based on SEQRES records: (download)
    >3df1U (U:)
    mpvikvrenepfdvalrrfkrscekagvlaevrrrefyekptterkrakasavkrhakkl
    arenarrtrly
    

    Sequence, based on observed residues (ATOM records): (download)
    >3df1U (U:)
    ikvrenepfdvalrrfkrscekagvlaevrrrefyekptterkrakasavk