PDB entry 3dll

View 3dll on RCSB PDB site
Description: The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning
Class: ribosome
Keywords: Ribosome, Antibiotic, oxazolidinone, Linezolid, Ribonucleoprotein, Ribosomal protein, RNA-binding, rRNA-binding, tRNA-binding, Methylation, Metal-binding, Zinc-finger
Deposited on 2008-06-27, released 2008-09-16
The last revision prior to the SCOPe 2.08 freeze date was dated 2015-07-22, with a file datestamp of 2015-07-17.
Experiment type: XRAY
Resolution: 3.5 Å
R-factor: N/A
AEROSPACI score: 0.05 (click here for full SPACI score report)

Chains and heterogens:

  • Chain '1':
    Compound: 50S ribosomal protein L33
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dll11
  • Chain '2':
    Compound: 50S ribosomal protein L34
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dll21
  • Chain '3':
    Compound: 50S ribosomal protein L35
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dll31
  • Chain '4':
    Compound: 50S ribosomal protein L36
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dll41
  • Chain 'A':
    Compound: 50S ribosomal protein L2
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed):
  • Chain 'B':
    Compound: 50S ribosomal protein L3
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dllb1
  • Chain 'C':
    Compound: 50S ribosomal protein L4
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dllc1
  • Chain 'D':
    Compound: 50S ribosomal protein L5
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dlld1
  • Chain 'E':
    Compound: 50S ribosomal protein L6
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dlle1, d3dlle2
  • Chain 'F':
    Compound: 50S ribosomal protein L11
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed):
  • Chain 'G':
    Compound: 50S ribosomal protein L13
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dllg1
  • Chain 'H':
    Compound: 50S ribosomal protein L14
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dllh1
  • Chain 'I':
    Compound: 50S ribosomal protein L15
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dlli1
  • Chain 'J':
    Compound: 50S ribosomal protein L16
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dllj1
  • Chain 'K':
    Compound: 50S ribosomal protein L17
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dllk1
  • Chain 'L':
    Compound: 50S ribosomal protein L18
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dlll1
  • Chain 'M':
    Compound: 50S ribosomal protein L19
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dllm1
  • Chain 'N':
    Compound: 50S ribosomal protein L20
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dlln1
  • Chain 'O':
    Compound: 50S ribosomal protein L21
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dllo1
  • Chain 'P':
    Compound: 50S ribosomal protein L22
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dllp1
  • Chain 'Q':
    Compound: 50S ribosomal protein L23
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dllq1
  • Chain 'R':
    Compound: 50S ribosomal protein L24
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dllr1
  • Chain 'S':
    Compound: 50S ribosomal protein L25
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dlls1
  • Chain 'T':
    Compound: 50S ribosomal protein L27
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dllt1
  • Chain 'U':
    Compound: 50S ribosomal protein L28
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dllu1
  • Chain 'V':
    Compound: 50S ribosomal protein L29
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dllv1
  • Chain 'W':
    Compound: 50S ribosomal protein L30
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dllw1
  • Chain 'X':
    Compound: rRNA-23S ribosomal RNA
    Species: Deinococcus radiodurans [TaxId:1299]
  • Chain 'Y':
    Compound: 50S ribosomal protein L32
    Species: Deinococcus radiodurans [TaxId:1299]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3dlly1
  • Chain 'Z':
    Compound: rRNA-5S ribosomal RNA
    Species: Deinococcus radiodurans [TaxId:1299]
  • Heterogens: ZN, MG, ZLD

PDB Chain Sequences:

  • Chain '1':
    Sequence, based on SEQRES records: (download) 
    >3dll1 (1:)
makdgpriivkmessagtgfyytttknrrntqaklelkkydpvakkhvvfrekkv

    Sequence, based on observed residues (ATOM records): (download) 
    >3dll1 (1:)
akdgpriivkmessagtgfyytttknrrntqaklelkkydpvakkhvvfrekk

  • Chain '2':
    Sequence, based on SEQRES records: (download) 
    >3dll2 (2:)
mkrtyqpnnrkrakthgfrarmktksgrnilarrrakgrhqltvsde

    Sequence, based on observed residues (ATOM records): (download) 
    >3dll2 (2:)
mkrtyqpnnrkrakthgfrarmktksgrnilarrrakgrhqltvsd

  • Chain '3':
    Sequence, based on SEQRES records: (download) 
    >3dll3 (3:)
mpkmkthkmakrrikitgtgkvmafksgkrhqntgksgdeirgkgkgfvlakaewarmkl
mlprgk

    Sequence, based on observed residues (ATOM records): (download) 
    >3dll3 (3:)
pkmkthkmakrrikitgtgkvmafksgkrhqntgksgdeirgkgkgfvlakaewarmklm
lpr

  • Chain '4':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >3dll4 (4:)
mkvrssvkkmcdnckvvrrhgrvlvicsnvkhkqrqg

  • Chain 'A':
    No sequence available.

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >3dllB (B:)
mkgilgtkigmtqiwkndraipvtvvlagpcpivqrktaqtdgyeavqigyapkaerkvn
kpmqghfakagvaptrilrefrgfapdgdsvnvdifaegekidatgtskgkgtqgvmkrw
nfaggpashgskkwhrrpgsigqrktpgrvykgkrmaghmgmervtvqnlevveiragen
lilvkgaipgangglvvlrsaakasaakggk

    Sequence, based on observed residues (ATOM records): (download) 
    >3dllB (B:)
mkgilgtkigmtqiwkndraipvtvvlagpcpivqrktaqtdgyeavqigyapkaerkvn
kpmqghfakagvaptrilrefrgfapdgdsvnvdifaegekidatgtskgkgtqgvmkrw
nfaggpashgskkwhrrpgsigqrktpgrvykgkrmaghmgmervtvqnlevveiragen
lilvkgaipgangglvvlrsaakas

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >3dllC (C:)
maqinvigqnggrtielplpevnsgvlhevvtwqlasrrrgtastrtraqvsktgrkmyg
qkgtgnarhgdrsvptfvgggvafgpkprsydytlprqvrqlglamaiasrqeggklvav
dgfdiadaktknfiswakqngldgtekvllvtddentrraarnvswvsvlpvagvnvydi
lrhdrlvidaaaleiveeeageeqq

    Sequence, based on observed residues (ATOM records): (download) 
    >3dllC (C:)
aqinvigqnggrtielplpevnsgvlhevvtwqlasrrrgtastrtraqvsktgrkmygq
kgtgnarhgdrsvptfvgggvafgpkprsydytlprqvrqlglamaiasrqeggklvavd
gfdiadaktknfiswakqngldgtekvllvtddentrraarnvswvsvlpvagvnvydil
rhdrlvidaaaleivee

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >3dllD (D:)
mqqlktkyndqvrpalmqqfgyssvmavpriekivvneglgsskedskaidkaakelali
tlqkpiitkakksisnfklrqgmpvgikvtlrgermyvflekliniglprirdfrginpn
afdgrgnynlgikeqlifpeitydmvdktrgmditivttaktdeearallqsmglpfrkq

    Sequence, based on observed residues (ATOM records): (download) 
    >3dllD (D:)
qlktkyndqvrpalmqqfgyssvmavpriekivvneglgsskedskaidkaakelalitl
qkpiitkakksisnfklrqgmpvgikvtlrgermyvflekliniglprirdfrginpnaf
dgrgnynlgikeqlifpeitydmvdktrgmditivttaktdeearallqsmglpfrk

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >3dllE (E:)
msrigkqpiavpsgvtvnaqdgvfkvkgpkgeltvpynteltvrqdgdqllverpsdaqk
hralhgltrtlvanavkgvsdgytinlelrgvgfrakltgkalemnigyshpviieppag
vtfavpeptridvsgidkqlvgqvaanvrkvrkpdayhgkgvrfvgeqialkagkagatg
gkgkk

    Sequence, based on observed residues (ATOM records): (download) 
    >3dllE (E:)
gkqpiavpsgvtvnaqdgvfkvkgpkgeltvpynteltvrqdgdqllverpsdaqkhral
hgltrtlvanavkgvsdgytinlelrgvgfrakltgkalemnigyshpviieppagvtfa
vpeptridvsgidkqlvgqvaanvrkvrkpdayhgkgvrfvgeqialkagk

  • Chain 'F':
    No sequence available.

  • Chain 'G':
    Sequence, based on SEQRES records: (download) 
    >3dllG (G:)
mafpdtdvspprggpsspakspllrsfkvktyipkndeqnwvvvdasgvplgrlatlias
rirgkhrpdftpnmiqgdfvvvinaaqvaltgkklddkvytrytgyqgglktetareals
khperviehavfgmlpkgrqgramhtrlkvyagethphsaqkpqvlktqplevk

    Sequence, based on observed residues (ATOM records): (download) 
    >3dllG (G:)
ktyipkndeqnwvvvdasgvplgrlatliasrirgkhrpdftpnmiqgdfvvvinaaqva
ltgkklddkvytrytgyqgglktetarealskhperviehavfgmlpkgrqgramhtrlk
vyagethphsaqkpqvlktqpl

  • Chain 'H':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >3dllH (H:)
mimpqsrldvadnsgareimcirvlnsgiggkglttggggnkryahvgdiivasvkdaap
rgavkagdvvkavvvrtshaikradgstirfdrnaaviinnqgeprgtrvfgpvarelrd
rrfmkivslapevl

  • Chain 'I':
    Sequence, based on SEQRES records: (download) 
    >3dllI (I:)
mklhdlkptpgsrkdrkrvgrgpggtdktagrghkgqksrsgagkgaffeggrsrliarl
pkrgfnnvgttyevvklsqlqdledttfdrdtleayrlvrrknrpvkllasgeisravtv
hvdaasaaaikaveaaggrvvlpevqtqqddaqkae

    Sequence, based on observed residues (ATOM records): (download) 
    >3dllI (I:)
hdlkptpgsrkdrkrvgrgpggtdktagrghkgqksrsgagkgaffeggrsrliarlpkr
gfnnvgttyevvklsqlqdledttfdrdtleayrlvrrknrpvkllasgeisravtvhvd
aasaaaikaveaaggrvvlpe

  • Chain 'J':
    Sequence, based on SEQRES records: (download) 
    >3dllJ (J:)
mmllpkrtkfrkqfrgrmtgdakggdyvafgdygliamepawiksnqieacrivmsrhfr
rggkiyirifpdkpvtkkpaetrmgkgkgaveywvsvvkpgrvmfevagvteeqakeafr
laghklpiqtkmvkrevydeaq

    Sequence, based on observed residues (ATOM records): (download) 
    >3dllJ (J:)
krtkfrkqfrgrmtgdakggdyvafgdygliamepawiksnqieacrivmsrhfrrggki
yirifpdkpvtkkpaetrmgkgkgaveywvsvvkpgrvmfevagvteeqakeafrlaghk
lpiqtkmvkrevydea

  • Chain 'K':
    Sequence, based on SEQRES records: (download) 
    >3dllK (K:)
mrhgkagrklnrnssarvalaraqatallregriqttltkakelrpfveqlittakggdl
hsrrlvaqdihdkdvvrkvmdevapkyaerpggytrilrvgtrrgdgvtmalielv

    Sequence, based on observed residues (ATOM records): (download) 
    >3dllK (K:)
hgkagrklnrnssarvalaraqatallregriqttltkakelrpfveqlittakggdlhs
rrlvaqdihdkdvvrkvmdevapkyaerpggytrilrvgtrrgdgvtmaliel

  • Chain 'L':
    Sequence, based on SEQRES records: (download) 
    >3dllL (L:)
matattirrklrtrrkvrtttaasgrlrlsvyrsskhiyaqiiddsrgqtlaaassaalk
sgnktdtaaavgkalaaaaaekgikqvvfdrgsykyhgrvkaladaareggldf

    Sequence, based on observed residues (ATOM records): (download) 
    >3dllL (L:)
rrklrtrrkvrtttaasgrlrlsvyrsskhiyaqiiddsrgqtlaaassaalksgnktdt
aaavgkalaaaaaekgikqvvfdrgsykyhgrvkaladaaregg

  • Chain 'M':
    Sequence, based on SEQRES records: (download) 
    >3dllM (M:)
mqthikinrgellrgieqdhtrqlpdfrpgdtvrvdtkvregnrtrsqafegvviaings
gsrksftvrkisfgegvervfpfasplvnqvtivergkvrraklyylrelrgkaariksd
rsrvmkdaaraqqdkanasasqaaaaqadvtvisaapevapetqge

    Sequence, based on observed residues (ATOM records): (download) 
    >3dllM (M:)
qthikinrgellrgieqdhtrqlpdfrpgdtvrvdtkvregnrtrsqafegvviaingsg
srksftvrkisfgegvervfpfasplvnqvtivergkvrraklyylre

  • Chain 'N':
    Sequence, based on SEQRES records: (download) 
    >3dllN (N:)
mpraktgivrrrrhkkvlkrakgfwgsrskqyrnafqtllnaatyeyrdrrnkkrdfrrl
wiqrinagarlhgmnystfinglkranidlnrkvladiaarepeafkalvdasrnarq

    Sequence, based on observed residues (ATOM records): (download) 
    >3dllN (N:)
praktgivrrrrhkkvlkrakgfwgsrskqyrnafqtllnaatyeyrdrrnkkrdfrrlw
iqrinagarlhgmnystfinglkranidlnrkvladiaarepeafkalvdasrnarq

  • Chain 'O':
    Sequence, based on SEQRES records: (download) 
    >3dllO (O:)
mfaiiqtggkqyrvsegdvirveslqgeagdkvelkalfvggeqtvfgedagkytvqaev
vehgrgkkiyirkyksgvqyrrrtghrqnftaikilgiqg

    Sequence, based on observed residues (ATOM records): (download) 
    >3dllO (O:)
iqtggkqyrvsegdvirveslqgeagdkvelkalfvggeqtvfgedagkytvqaevvehg
rgkkiyirkyksgvqyrrrtghrqnftaikilgi

  • Chain 'P':
    Sequence, based on SEQRES records: (download) 
    >3dllP (P:)
mtapeqtfrnkkqrkqqvklrkpgfavakyvrmsprkvrlvvdvirgksvqdaedllrfi
prsasepvakvlnsakanalhndemledrlfvkeayvdagptlkrliprargsaniikkr
tshitiivaekgnk

    Sequence, based on observed residues (ATOM records): (download) 
    >3dllP (P:)
frnkkqrkqqvklrkpgfavakyvrmsprkvrlvvdvirgksvqdaedllrfiprsasep
vakvlnsakanalhndemledrlfvkeayvdagptlkrliprargsaniikkrtshitii
vaekgnk

  • Chain 'Q':
    Sequence, based on SEQRES records: (download) 
    >3dllQ (Q:)
mshydilqapvisekaysamergvysfwvspkatkteikdaiqqafgvrvigistmnvpg
krkrvgrfigqrndrkkaivrlaegqsiealagqa

    Sequence, based on observed residues (ATOM records): (download) 
    >3dllQ (Q:)
shydilqapvisekaysamergvysfwvspkatkteikdaiqqafgvrvigistmnvpgk
rkrvgrfigqrndrkkaivrlaegqsiealagq

  • Chain 'R':
    Sequence, based on SEQRES records: (download) 
    >3dllR (R:)
mprpsagshhndklhfkkgdtvivlsgkhkgqtgkvllalprdqkvvvegvnvitknvkp
smtnpqggqeqrelalhaskvalvdpetgkatrvrkqivdgkkvrvavasgktid

    Sequence, based on observed residues (ATOM records): (download) 
    >3dllR (R:)
psagshhndklhfkkgdtvivlsgkhkgqtgkvllalprdqkvvvegvnvitknvkpsmt
npqggqeqrelalhaskvalvdpetgkatrvrkqivdgkkvrvavasgkt

  • Chain 'S':
    Sequence, based on SEQRES records: (download) 
    >3dllS (S:)
meltakprtpkqkldesmiaavaynkennvsfaldrkafdrafrqqsttglfditvegge
tfpalvkavqmdkrkrapihvdfymvtygepvevsvpvhttgrsqgevqgglvdivvhnl
qivapgprripqelvvdvtkmnigdhitagdiklpegctlaadpeltvvsvlpprltaee
leaevqaaqvaglvaagelseeaaeavlegdasleevkaeasednagtdsednsdaq

    Sequence, based on observed residues (ATOM records): (download) 
    >3dllS (S:)
meltakprtpkqkldesmiaavaynkennvsfaldrkafdrafrqqsttglfditvegge
tfpalvkavqmdkrkrapihvdfymvtygepvevsvpvhttgrsqgevqgglvdivvhnl
qivapgprripqelvvdvtkmnigdhitagdiklpegctlaadpeltvvsvlppr

  • Chain 'T':
    Sequence, based on SEQRES records: (download) 
    >3dllT (T:)
mahkkgvgsskngrdsnpkylgvkkfggevvkagnilvrqrgtkfkagqgvgmgrdhtlf
alsdgkvvfinkgkgarfisieaaqtevaad

    Sequence, based on observed residues (ATOM records): (download) 
    >3dllT (T:)
ahkkgvgsskngrdsnpkylgvkkfggevvkagnilvrqrgtkfkagqgvgmgrdhtlfa
lsdgkvvfinkgkgarfisieaaq

  • Chain 'U':
    Sequence, based on SEQRES records: (download) 
    >3dllU (U:)
msrecyltgkknlvvnsvirrgkaradggvgrkttgitkrvqranlhkkairengqvktv
wlsanalrtlskgpykgieli

    Sequence, based on observed residues (ATOM records): (download) 
    >3dllU (U:)
tgkknlvvnsvirrgkaradggvgrkttgitkrvqranlhkkairengqvktvwlsanal
rtlskgpykgie

  • Chain 'V':
    Sequence, based on SEQRES records: (download) 
    >3dllV (V:)
mkpsemrnlqatdfakeidarkkelmelrfqaaagqlaqphrvrqlrrevaqlntvkael
arkgeqq

    Sequence, based on observed residues (ATOM records): (download) 
    >3dllV (V:)
mkpsemrnlqatdfakeidarkkelmelrfqaaagqlaqphrvrqlrrevaqlntvkael
arkgeq

  • Chain 'W':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >3dllW (W:)
mkiklvrsvigrpgnqvktvqalglrkigdsrevsdtpavrgmvktvkhllevqe

  • Chain 'X':
    No sequence available.

  • Chain 'Y':
    Sequence, based on SEQRES records: (download) 
    >3dllY (Y:)
makhpvpkkktskskrdmrrshhaltapnltecpqchgkklshhicpncgyydgrqvlav

    Sequence, based on observed residues (ATOM records): (download) 
    >3dllY (Y:)
akhpvpkkktskskrdmrrshhaltapnltecpqchgkklshhicpncgyydgrqvla

  • Chain 'Z':
    No sequence available.