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 2.06 freeze date was dated 2014-12-10, with a file datestamp of 2014-12-05.
Experiment type: XRAY
Resolution: 3.5 Å
R-factor: 0.269
AEROSPACI score: 0.04 (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 2.06: d3df1b1
  • Chain 'C':
    Compound: 30S ribosomal protein S3
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3df1c1, d3df1c2
  • Chain 'D':
    Compound: 30S ribosomal protein S4
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3df1d1
  • Chain 'E':
    Compound: 30S ribosomal protein S5
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3df1e1, d3df1e2
  • Chain 'F':
    Compound: 30S ribosomal protein S6
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3df1f1
  • Chain 'G':
    Compound: 30S ribosomal protein S7
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3df1g1
  • Chain 'H':
    Compound: 30S ribosomal protein S8
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3df1h1
  • Chain 'I':
    Compound: 30S ribosomal protein S9
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3df1i1
  • Chain 'J':
    Compound: 30S ribosomal protein S10
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3df1j1
  • Chain 'K':
    Compound: 30S ribosomal protein S11
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3df1k1
  • Chain 'L':
    Compound: 30S ribosomal protein S12
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3df1l1
  • Chain 'M':
    Compound: 30S ribosomal protein S13
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3df1m1
  • Chain 'N':
    Compound: 30S ribosomal protein S14
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3df1n1
  • Chain 'O':
    Compound: 30S ribosomal protein S15
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3df1o1
  • Chain 'P':
    Compound: 30S ribosomal protein S16
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3df1p1
  • Chain 'Q':
    Compound: 30S ribosomal protein S17
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3df1q1
  • Chain 'R':
    Compound: 30S ribosomal protein S18
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3df1r1
  • Chain 'S':
    Compound: 30S ribosomal protein S19
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3df1s1
  • Chain 'T':
    Compound: 30S ribosomal protein S20
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3df1t1
  • Chain 'U':
    Compound: 30S ribosomal protein S21
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: 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