PDB entry 1qvf

View 1qvf on RCSB PDB site
Description: Structure of a deacylated tRNA minihelix bound to the E site of the large ribosomal subunit of Haloarcula marismortui
Class: ribosome
Keywords: ribosome 50S, PROTEIN-PROTEIN COMPLEX, RNA-RNA COMPLEX, PROTEIN-RNA COMPLEX
Deposited on 2003-08-27, released 2003-11-11
The last revision prior to the SCOPe 2.06 freeze date was dated 2009-02-24, with a file datestamp of 2009-03-01.
Experiment type: XRAY
Resolution: 3.1 Å
R-factor: 0.196
AEROSPACI score: 0.24 (click here for full SPACI score report)

Chains and heterogens:

  • Chain '0':
    Compound: 23S ribosomal RNA
    Species: Haloarcula marismortui [TaxId:2238]
  • Chain '1':
    Compound: 50S ribosomal protein L39e
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d1qvf1_
  • Chain '2':
    Compound: 50S ribosomal protein L44E
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d1qvf2_
  • Chain '3':
    Compound: Deacylated tRNA minihelix
  • Chain '9':
    Compound: 5S ribosomal RNA
    Species: Haloarcula marismortui [TaxId:2238]
  • Chain 'A':
    Compound: 50S ribosomal protein L2P
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d1qvfa1, d1qvfa2
  • Chain 'B':
    Compound: 50S ribosomal protein L3P
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P20279 (0-336)
      • conflict (309)
    Domains in SCOPe 2.06: d1qvfb_
  • Chain 'C':
    Compound: 50S ribosomal protein L4E
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d1qvfc_
  • Chain 'D':
    Compound: 50S ribosomal protein L5P
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d1qvfd_
  • Chain 'E':
    Compound: 50S ribosomal protein L6P
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d1qvfe1, d1qvfe2
  • Chain 'F':
    Compound: 50S ribosomal protein L7Ae
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d1qvff_
  • Chain 'G':
    Compound: 50S ribosomal protein L10e
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d1qvfg_
  • Chain 'H':
    Compound: L10 Ribosomal Protein
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed):
    • PDB 1QVF (0-166)
    Domains in SCOPe 2.06: d1qvfh_
  • Chain 'I':
    Compound: 50S ribosomal protein L13P
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d1qvfi_
  • Chain 'J':
    Compound: 50S ribosomal protein L14P
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d1qvfj_
  • Chain 'K':
    Compound: 50S ribosomal protein L15P
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d1qvfk_
  • Chain 'L':
    Compound: L15 Ribosomal Protein
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed):
    • PDB 1QVF (0-193)
    Domains in SCOPe 2.06: d1qvfl_
  • Chain 'M':
    Compound: 50S ribosomal protein L18P
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d1qvfm_
  • Chain 'N':
    Compound: 50S ribosomal protein L18e
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d1qvfn_
  • Chain 'O':
    Compound: 50S ribosomal protein L19e
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P14119 (0-End)
      • conflict (70)
    Domains in SCOPe 2.06: d1qvfo_
  • Chain 'P':
    Compound: 50S ribosomal protein L21e
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d1qvfp_
  • Chain 'Q':
    Compound: 50S ribosomal protein L22P
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d1qvfq_
  • Chain 'R':
    Compound: 50S ribosomal protein L23P
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d1qvfr_
  • Chain 'S':
    Compound: 50S ribosomal protein L24P
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d1qvfs_
  • Chain 'T':
    Compound: 50S ribosomal protein L24e
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d1qvft_
  • Chain 'U':
    Compound: 50S ribosomal protein L29P
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d1qvfu_
  • Chain 'V':
    Compound: 50S ribosomal protein L30P
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d1qvfv_
  • Chain 'W':
    Compound: 50S ribosomal protein L31e
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d1qvfw_
  • Chain 'X':
    Compound: 50S ribosomal protein L32e
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d1qvfx_
  • Chain 'Y':
    Compound: L37Ae 50S ribosomal protein
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed):
    • PDB 1QVF (0-72)
    Domains in SCOPe 2.06: d1qvfy_
  • Chain 'Z':
    Compound: 50S ribosomal protein L37e
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d1qvfz_
  • Heterogens: MG, K, NA, CL, CD, HOH

PDB Chain Sequences:

  • Chain '0':
    No sequence available.

  • Chain '1':
    Sequence, based on SEQRES records: (download) 
    >1qvf1 (1:)
gkkskatkkrlakldnqnsrvpawvmlktdevqrnhkrrhwrrndtde

    Sequence, based on observed residues (ATOM records): (download) 
    >1qvf1 (1:)
gkkskatkkrlakldnqnsrvpawvmlktdernhkrrhwrrndtde

  • Chain '2':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >1qvf2 (2:)
mqmprrfntycphcnehqehevekvrsgrqtgmkwidrqrernsgigndgkfskvpggdk
ptkktdlkyrcgecgkahlregwragrlefqe

  • Chain '3':
    No sequence available.

  • Chain '9':
    No sequence available.

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >1qvfA (A:)
grriqgqrrgrgtstfrapshrykadlehrkvedgdviagtvvdiehdparsapvaavef
edgdrrlilapegvgvgdelqvgvdaeiapgntlplaeipegvpvcnvesspgdggkfar
asgvnaqllthdrnvavvklpsgemkrldpqcratigvvggggrtdkpfvkagnkhhkmk
argtkwpnvrgvamnavdhpfggggrqhpgkpksisrnappgrkvgdiaskrtgrggne

    Sequence, based on observed residues (ATOM records): (download) 
    >1qvfA (A:)
grriqgqrrgrgtstfrapshrykadlehrkvedgdviagtvvdiehdparsapvaavef
edgdrrlilapegvgvgdelqvgvdaeiapgntlplaeipegvpvcnvesspgdggkfar
asgvnaqllthdrnvavvklpsgemkrldpqcratigvvggggrtdkpfvkagnkhhkmk
argtkwpnvrgvamnavdhpfggggrqhpgkpksisrnappgrkvgdiaskrtgrgg

  • Chain 'B':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >1qvfB (B:)
pqpsrprkgslgfgprkrstsetprfnswpsddgqpgvqgfagykagmthvvlvndepns
pregmeetvpvtvietppmravalrayedtpygqrpltevwtdefhseldrtldvpedhd
pdaaeeqirdaheagdlgdlrlithtvpdavpsvpkkkpdvmetrvgggsvsdrldhald
ivedggehamndifrageyadvagvtkgkgtqgpvkrwgvqkrkgkharqgwrrrignlg
pwnpsrvrstvpqqgqtgyhqrtelnkrlidigegdeptvdggfvnygevdgpytlvkgs
vpgpdkrlvrfrpavrpndqprldpevryvsnesnqg

  • Chain 'C':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >1qvfC (C:)
mqatiydldgntdgevdlpdvfetpvrsdligkavraaqanrkqdygsdeyaglrtpaes
fgsgrgqahvpkldgrarrvpqavkgrsahppktekdrsldlndkerqlavrsalaatad
adlvadrghefdrdevpvvvsddfedlvktqevvsllealdvhadidradetkikagqgs
argrkyrrpasilfvtsdepstaarnlagadvatasevntedlapggapgrltvftesal
aevaer

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >1qvfD (D:)
ssesesggdfhemrepriekvvvhmgighggrdlanaedilgeitgqmpvrtkakrtvge
fdiregdpigakvtlrdemaeeflqtalplaelatsqfddtgnfsfgveehtefpsqeyd
psigiygldvtvnlvrpgyrvakrdkasrsiptkhrlnpadavafiestydvevse

    Sequence, based on observed residues (ATOM records): (download) 
    >1qvfD (D:)
fhemrepriekvvvhmgighanaedilgeitgqmpvrtkakrtvgefdiregdpigakvt
lrdemaeeflqtalplaelatsqfddtgnfsfgldvtvnlvrpgyrvakrdkasrsiptk
hrlnpadavafiestydvev

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >1qvfE (E:)
prveleipedvdaeqdhlditvegdngsvtrrlwypdidvsvdgdtvviesdednaktms
tigtfqshienmfhgvtegweygmevfyshfpmqvnvegdevvienflgekaprrttihg
dtdveidgeeltvsgpdieavgqtaadieqltrindkdvrvfqdgvyitrkpnrgda

    Sequence, based on observed residues (ATOM records): (download) 
    >1qvfE (E:)
prveleipedvdaeqdhlditvegdngsvtrrlwypdidvsvdgdtvviesdednaktms
tigtfqshienmfhgvtegweygmevfyshfpmqvnvegdevvienflgekaprrttihg
dtdveidgeeltvsgpdieavgqtaadieqltrindkdvrvfqdgvyitrkp

  • Chain 'F':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >1qvfF (F:)
pvyvdfdvpadleddalealevardtgavkkgtnettksiergsaelvfvaedvqpeeiv
mhipeladekgvpfifveqqddlghaaglevgsaaaavtdagaaatvleeiadkveelr

  • Chain 'G':
    Sequence, based on SEQRES records: (download) 
    >1qvfG (G:)
msaeserktetipewkqeevdaivemiesyesvgvvniagipsrqlqdmrrdlhgtaelr
vsrntlleralddvddgledlngyitgqvgligtddnpfslfqeleasktpapigageva
pndivipegdtgvdpgpfvgelqsvgadariqegsiqvlsdstvldtgeevsqelsnvln
elgiepkevgldlravfadgvlfepeeleldideyrsdiqaaagrafnlsvnadyptatt
aptmlqsdrgnakslalqaaiedpevvpdlvskadaqvralasqiddeealpeelqgvea
dvateeptddqdddtaseddadaddaaeeadddddddedagdalgamf

    Sequence, based on observed residues (ATOM records): (download) 
    >1qvfG (G:)
ipewkqeevdaivemiesrntlleraldd

  • Chain 'H':
    Sequence, based on SEQRES records: (download) 
    >1qvfH (H:)
kpgamyrnsskpaytrreyisgipgkkiaqfdmgnngagptypaqvelvvekpvqirhna
leaarvaanryvqnsgaaanykfrirkfpfhvirenkaaaaaaaaaaadgmrapfgkpvg
taarvhganhifiawvnpdpnveeawrrakmkvtptinidsspagna

    Sequence, based on observed residues (ATOM records): (download) 
    >1qvfH (H:)
kpgamyrnsskpaytrreyisgipgkkiaqfdmgnngagptypaqvelvvekpvqirhna
leaarvaanryvqnsgaaanykfrirkfpfhvirenkdgmrapfgkpvgtaarvhganhi
fiawvnpdpnveeawrrakmkvtptinidsspagna

  • Chain 'I':
    Sequence, based on SEQRES records: (download) 
    >1qvfI (I:)
msvaefdadvivdardcimgrvasqvaeqaldgetvavvnaeravitgreeqivekyekr
vdigndngyfypkrpdgifkrtirgmlphkkqrgreafesvrvylgnpydedgevldgts
ldrlsnikfvtlgeisetlganktw

    Sequence, based on observed residues (ATOM records): (download) 
    >1qvfI (I:)
aefdadvivdardcimgrvasqvaeqaldgetvavvnaeravitgreeqivekyekrvdi
gndngyfypkrpdgifkrtirgmlphkkqrgreafesvrvylgnpydedgevldgtsldr
lsnikfvtlgeisetlganktw

  • Chain 'J':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >1qvfJ (J:)
mealgadvtqglekgslitcadntgarelkvisvhgysgtknrhpkaglgdkitvsvtkg
tpemrrqvleavvvrqrkpirrpdgtrvkfednaavivdenedprgtelkgpiarevaqr
fgsvasaatmiv

  • Chain 'K':
    Sequence, based on SEQRES records: (download) 
    >1qvfK (K:)
tskkkrqrgsrthgggshknrrgaghrggrgdagrdkhefhnheplgksgfkrpqkvqee
aatidvreidenvtllaaddvaevedggfrvdvrdvveeaddadyvkvlgagqvrheltl
iaddfsegarekvegaggsveltdlgeerqaeaeetedadadee

    Sequence, based on observed residues (ATOM records): (download) 
    >1qvfK (K:)
tskkkrqrgsrthgggshknrrgaghrggrgdagrdkhefhnheplgksgfkrpqkvqee
aatidvreidenvtllaaddvaefrvdvrdvveeaddadyvkvlgagqvrheltliaddf
segarekvegaggsveltdlgeerq

  • Chain 'L':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >1qvfL (L:)
arsaysyireawkrpkegqiaelmwhrmqewrnepavvrierptrldrarslgykakqgi
ivvrvairkgssrrtrfnkgrrskrmmvnritrkkniqriaeeranrkfpnlrvlnsysv
gedgrhkwhevilidpdhpaiksddqlswisrtrhrlrtfrgltsagrrcrglrgqgkgs
ekvrpslrvngaka

  • Chain 'M':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >1qvfM (M:)
atgprykvpmrrrreartdyhqrlrllksgkprlvarksnkhvraqlvtlgpngddtlas
ahssdlaeygweaptgnmpsayltgllaglraqeagveeavldiglnsptpgskvfaiqe
gaidagldiphnddvladwqrtrgahiaeydeqleeplysgdfdaadlpehfdelretll
dgdiel

  • Chain 'N':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >1qvfN (N:)
sktnprlssliadlksaarssggavwgdvaerlekprrthaevnlgrieryaqedetvvv
pgkvlgsgvlqkdvtvaavdfsgtaetkidqvgeavsleqaiennpegshvrvir

  • Chain 'O':
    Sequence, based on SEQRES records: (download) 
    >1qvfO (O:)
tdlsaqkrlaadvldvgknrvwfnperqgdiadaitredvrelvdegaiqakdkkgnsrg
rarerqkkrakghqkgagsrkgkagarqnskedwesriraqrtklrelrdegtlsssqyr
dlydkagggefdsvadleryidanhgda

    Sequence, based on observed residues (ATOM records): (download) 
    >1qvfO (O:)
tdlsaqkrlaadvldvgknrvwfnperqgdiadaitredvrelvdegaiqakdkkgnsrg
rarerqkkrakghqkgagsrkgkagarqnskedwesriraqrtklrelrdegtlsssqyr
dlydkagggefdsvadleryida

  • Chain 'P':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >1qvfP (P:)
pssngplegtrgklknkprdrgtsppqraveefddgekvhlkidpsvpngrfhprfdgqt
gtvegkqgdaykvdivdggkektiivtaahlrrqe

  • Chain 'Q':
    Sequence, based on SEQRES records: (download) 
    >1qvfQ (Q:)
gisysveadpdttakamlrerqmsfkhskaiareikgktageavdyleaviegdqpvpfk
qhnsgvghkskvdgwdagrypekaskafldllenavgnadhqgfdgeamtikhvaahkvg
eqqgrkpramgrasawnspqvdvelileepeved

    Sequence, based on observed residues (ATOM records): (download) 
    >1qvfQ (Q:)
gisysveadpdttakamlrerqmsfkhskaiareikgktageavdyleaviegdqpvpfk
qhnsgvghkskvdgwdagrypekaskafldllenavgnadhqgfdgeamtikhvaahkvg
eqqgrkpramgrasawnspqvdvelileep

  • Chain 'R':
    Sequence, based on SEQRES records: (download) 
    >1qvfR (R:)
swdvikhphvtekamndmdfqnklqfavddraskgevadaveeqydvtveqvntqntmdg
ekkavvrlsedddaqevasrigvf

    Sequence, based on observed residues (ATOM records): (download) 
    >1qvfR (R:)
swdvikhphvtekamndmdfqnklqfavddraskgevadaveeqydvtveqvntqntmdg
ekkavvrlsedddaqevasri

  • Chain 'S':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >1qvfS (S:)
skqpdkqrksqrraplherhkqvratlsadlreeygqrnvrvnagdtvevlrgdfageeg
evinvdldkavihvedvtlektdgeevprpldtsnvrvtdldledekrearleseddsa

  • Chain 'T':
    Sequence, based on SEQRES records: (download) 
    >1qvfT (T:)
prtrecdycgtdiepgtgtmfvhkdgatthfcsskcennadlgrearnlewtdtargeag
eaedea

    Sequence, based on observed residues (ATOM records): (download) 
    >1qvfT (T:)
recdycgtdiepgtgtmfvhkdgatthfcsskcennadlgrearnlewtdtar

  • Chain 'U':
    Sequence, based on SEQRES records: (download) 
    >1qvfU (U:)
tvlhvqeirdmtpaereaelddlktellnaravqaaggapenpgrikelrkaiariktiq
geegdlqene

    Sequence, based on observed residues (ATOM records): (download) 
    >1qvfU (U:)
tvlhvqeirdmtpaereaelddlktellnaravqaaggapenpgrikelrkaiariktiq
geegd

  • Chain 'V':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >1qvfV (V:)
mhalvqlrgevnmhtdiqdtlemlnihhvnhctlvpetdayrgmvakvndfvafgepsqe
tletvlatraeplegdadvddewvaehtdyddisglafallseettlreqglsptlrlhp
prgghdgvkhpvkeggqlgkhdtegiddlleamr

  • Chain 'W':
    Sequence, based on SEQRES records: (download) 
    >1qvfW (W:)
sasdfeervvtiplrdaraepnhkradkamilirehlakhfsvdedavrldpsineaawa
rgrantpskirvraarfeeegeaiveaetae

    Sequence, based on observed residues (ATOM records): (download) 
    >1qvfW (W:)
ervvtiplrdaraepnhkradkamilirehlakhfsvdedavrldpsineaawargrant
pskirvraarfeeegeaiveae

  • Chain 'X':
    Sequence, based on SEQRES records: (download) 
    >1qvfX (X:)
adneedveaeeeyteltdisgvgpskaeslreagfesvedvrgadqsaladvsgignala
arikadvggleveseteaeveeeggeeapdedvetelqargltektpdlsdedarlltqr
hrvgkpqfnrqdhhkkkrvstswrkprgqlskqrrgikgkgdtveagfrsptavrgkhps
gfeevrvhnvddlegvdgdteavriaskvgarkrerieeeaedagirvlnptyvevevse

    Sequence, based on observed residues (ATOM records): (download) 
    >1qvfX (X:)
telqargltektpdlsdedarlltqrhrvgkpqfnrqdhhkkkrvstswrkprgqlskqr
rgikgkgdtveagfrsptavrgkhpsgfeevrvhnvddlegvdgdteavriaskvgarkr
erieeeaedagirvlnptyvev

  • Chain 'Y':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >1qvfY (Y:)
rtgrfgpryglkirvrvadveikhkkkhkcpvcgfkklkragtgiwmcghcgykiaggcy
qpetvagkavmka

  • Chain 'Z':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >1qvfZ (Z:)
tgagtpsqgkknttthtkcrrcgeksyhtkkkvcsscgfgksakrrdyewqskage