PDB entry 1yl3

View 1yl3 on RCSB PDB site
Description: Crystal structure of 70S ribosome with thrS operator and tRNAs. Large subunit. The coordinates for the small subunit are in the pdb entry 1YL4.
Class: ribosome
Keywords: ribosome, mRNA, translational operator
Deposited on 2005-01-19, released 2005-04-12
The last revision prior to the SCOP 1.73 freeze date was dated 2005-04-12, with a file datestamp of 2007-06-28.
Experiment type: XRAY
Resolution: 5.5 Å
R-factor: 0.307
AEROSPACI score: -0.13 (click here for full SPACI score report)

Chains and heterogens:

  • Chain '0':
    Compound: 50S ribosomal protein L17
    Species: Thermus thermophilus
    Database cross-references and differences (RAF-indexed): Domains in SCOP 1.73: d1yl301
  • Chain '1':
    Compound: 50S ribosomal protein L20
    Species: Thermus thermophilus
  • Chain '2':
    Compound: 50S ribosomal protein L21
    Species: Thermus thermophilus
  • Chain '3':
    Compound: 50S ribosomal protein L27
    Species: Thermus thermophilus
  • Chain '4':
    Compound: 50S ribosomal protein L31
    Species: Thermus thermophilus
  • Chain '5':
    Compound: 50S ribosomal protein L32
    Species: Thermus thermophilus
  • Chain '6':
    Compound: 50S ribosomal protein L33
    Species: Thermus thermophilus
  • Chain '7':
    Compound: 50S ribosomal protein L34
    Species: Thermus thermophilus
  • Chain '8':
    Compound: 50S ribosomal protein L35
    Species: Thermus thermophilus
  • Chain '9':
    Compound: 50S ribosomal protein L36
    Species: Thermus thermophilus
  • Chain 'A':
    Compound: 23S ribosomal RNA
    Species: Thermus thermophilus
  • Chain 'B':
    Compound: 5S ribosomal RNA
    Species: Thermus thermophilus
  • Chain 'C':
    Compound: 50s ribosomal protein l1
    Species: Thermus thermophilus
    Database cross-references and differences (RAF-indexed):
  • Chain 'D':
    Compound: 50S ribosomal protein L2
    Species: Thermus thermophilus
    Database cross-references and differences (RAF-indexed): Domains in SCOP 1.73: d1yl3d1, d1yl3d2
  • Chain 'E':
    Compound: 50S ribosomal protein L3
    Species: Thermus thermophilus
  • Chain 'F':
    Compound: 50S ribosomal protein L4
    Species: Thermus thermophilus
    Domains in SCOP 1.73: d1yl3f1
  • Chain 'G':
    Compound: 50S ribosomal protein L5
    Species: Thermus thermophilus
  • Chain 'H':
    Compound: 50S ribosomal protein L6
    Species: Thermus thermophilus
    Domains in SCOP 1.73: d1yl3h1, d1yl3h2
  • Chain 'I':
    Compound: 50S ribosomal protein L7/L12
    Species: Thermus thermophilus
    Domains in SCOP 1.73: d1yl3i1, d1yl3i2
  • Chain 'J':
    Compound: 50S ribosomal protein L7/L12
    Species: Thermus thermophilus
    Domains in SCOP 1.73: d1yl3j1, d1yl3j2
  • Chain 'K':
    Compound: 50S ribosomal protein L9
    Species: Thermus thermophilus
    Domains in SCOP 1.73: d1yl3k1, d1yl3k2
  • Chain 'L':
    Compound: 50S ribosomal protein L11
    Species: Thermus thermophilus
    Domains in SCOP 1.73: d1yl3l1, d1yl3l2
  • Chain 'M':
    Compound: 50S ribosomal protein L13
    Species: Thermus thermophilus
    Domains in SCOP 1.73: d1yl3m1
  • Chain 'N':
    Compound: 50S ribosomal protein L14
    Species: Thermus thermophilus
    Domains in SCOP 1.73: d1yl3n1
  • Chain 'O':
    Compound: 50S ribosomal protein L15
    Species: Thermus thermophilus
  • Chain 'P':
    Compound: 50S ribosomal protein L16
    Species: Thermus thermophilus
  • Chain 'Q':
    Compound: 50S ribosomal protein L18
    Species: Thermus thermophilus
  • Chain 'R':
    Compound: 50S ribosomal protein L19
    Species: Thermus thermophilus
    Domains in SCOP 1.73: d1yl3r1
  • Chain 'S':
    Compound: 50S ribosomal protein L22
    Species: Thermus thermophilus
    Database cross-references and differences (RAF-indexed): Domains in SCOP 1.73: d1yl3s1
  • Chain 'T':
    Compound: 50S ribosomal protein L23
    Species: Thermus thermophilus
    Domains in SCOP 1.73: d1yl3t1
  • Chain 'U':
    Compound: 50S ribosomal protein L24
    Species: Thermus thermophilus
    Domains in SCOP 1.73: d1yl3u1
  • Chain 'V':
    Compound: 50S general stress protein CTC (L25)
    Species: Thermus thermophilus
  • Chain 'W':
    Compound: 50S ribosomal protein L29
    Species: Thermus thermophilus
    Domains in SCOP 1.73: d1yl3w1
  • Chain 'X':
    Compound: 50S ribosomal protein L30
    Species: Thermus thermophilus
    Database cross-references and differences (RAF-indexed): Domains in SCOP 1.73: d1yl3x1

PDB Chain Sequences:

  • Chain '0':
    Sequence, based on SEQRES records: (download) 
    >1yl30 (0:)
mrhlksgrklnrhsshrlalyrnqaksllthgritttvpkakelrgfvdhlihlakrgdl
harrlvlrdlqdvklvrklfdeiapryrdrqggytrvlklaerrrgdgaplalvelve

    Sequence, based on observed residues (ATOM records): (download) 
    >1yl30 (0:)
sshrlalyrnqaksllthgritttvpkakelrgfvdhlihlakrgdlharrlvlrdlqdv
klvrklfdeiapryrdrqggytrvlklaerrrgdgaplalvelve

  • Chain '1':
    No sequence available.

  • Chain '2':
    No sequence available.

  • Chain '3':
    No sequence available.

  • Chain '4':
    No sequence available.

  • Chain '5':
    No sequence available.

  • Chain '6':
    No sequence available.

  • Chain '7':
    No sequence available.

  • Chain '8':
    No sequence available.

  • Chain '9':
    No sequence available.

  • Chain 'A':
    No sequence available.

  • Chain 'B':
    No sequence available.

  • Chain 'C':
    No sequence available.

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >1yl3D (D:)
qyriidfkrdkdgipgrvatieydpnrsanialinyadgekryiiapknlkvgmeimsgp
dadikignalplenipvgtlvhnielkpgrggqlvraagtsaqvlgkegkyvivrlasge
vrmilgkcratvgevgnggrtdkpfvkagnkhhkmkargtkwpnvrgvamnavdhpfg

    Sequence, based on observed residues (ATOM records): (download) 
    >1yl3D (D:)
qyriidfkrdkdgipgrvatieydpnrsanialinyadgekryiiapknlkvgmeimsgp
dadikignalplenipvgtlvhnielkpgrggqlvraagtsaqvlgkegkyvivrlasge
vrmilgkcratvgevgnggrtdkpfvkagnkhhkmkapnvrgvamnavdhpfg

  • Chain 'E':
    No sequence available.

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >1yl3F (F:)
meatiydldgntdgevdlpdvfetpvrsdligkavraaqanrkqdygsdeyaglrtpaes
fgsgrgqahvpkldgrarrvpqavkgrsahppktekdrsldlndkerqlavrsalaatad
adlvadrghefdrdevpvvvsddfedlvktqevvsllealdvhadidradetkikagqgs
argrkyrrpasilfvtsdepstaarnlagadvatasevntedlapggapgrltvftesal
aevaer

    Sequence, based on observed residues (ATOM records): (download) 
    >1yl3F (F:)
meatiydntdgevdlpdvfetpvrsdligkavraaqanrkqdygsdeyaglrtpaesfgs
grgqahrvpqavkgrsahppktekdrsldlndkerqlavrsalaatadvvvsddfedlvk
tqevvsllealdvhadidrlfvtsdepstaarnlagadvatasevntedlapgrltvfte
salaevaer

  • Chain 'G':
    No sequence available.

  • Chain 'H':
    Sequence, based on SEQRES records: (download) 
    >1yl3H (H:)
srvgkkpieipagvtvtvngntvtvkgpkgeltrtfhpdmtitvegnvitvtrpsdekhh
ralhgttrsllanmvegvskgyekalelvgvgyraskqgkklvlsvgyshpveiepeegl
eievpsqtkiivkgadkqrvgelaaniravrppepykgkgiryegelvrlkegktgk

    Sequence, based on observed residues (ATOM records): (download) 
    >1yl3H (H:)
pieipagvtvtvngntvtvkgpkgeltrtfhpdmtitvegnvitvtrpsdekhhralhgt
trsllanmvegvskgyekalelvgvgyraskqgkklvlsvgyshpveiepeegleievps
qtkiivkgadkqrvgelaaniravrppepykgkgiryegelvrl

  • Chain 'I':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >1yl3I (I:)
mtideiieaiekltvselaelvkkledkfgvtaaapvavaaapvagaaagaaqeektefd
vvlksfgqnkiqvikvvreitglglkeakdlvekagspdaviksgvskeeaeeikkklee
agaevelk

  • Chain 'J':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >1yl3J (J:)
mtideiieaiekltvselaelvkkledkfgvtaaapvavaaapvagaaagaaqeektefd
vvlksfgqnkiqvikvvreitglglkeakdlvekagspdaviksgvskeeaeeikkklee
agaevelk

  • Chain 'K':
    Sequence, based on SEQRES records: (download) 
    >1yl3K (K:)
mkviflkdvkgkgkkgeiknvadgyannflfkqglaieatpanlkaleaqkqkeqrqaae
elanakklkeqlekltvtipakageggrlfgsitskqiaeslqaqhglkldkrkielada
iralgytnvpvklhpevtatlkvhvteqk

    Sequence, based on observed residues (ATOM records): (download) 
    >1yl3K (K:)
mkviflkdvkgkgkkgeiknvadgyannflfkqglaieatpanlkaleaqkqkeqrqaae
elanakklkeqlekltvtipakagegrlfgsitskqiaeslqaqhglkldkrkieladai
ralgytnvpvklhpevtatlkvhvteqk

  • Chain 'L':
    Sequence, based on SEQRES records: (download) 
    >1yl3L (L:)
makkvaaqiklqlpagkatpappvgpalgqhgvnimefckrfnaetadkagmilpvvitv
yedksftfiiktppasfllkkaagiekgssepkrkivgkvtrkqieeiaktkmpdlnans
leaamkiiegtaksmgievvd

    Sequence, based on observed residues (ATOM records): (download) 
    >1yl3L (L:)
qiklqlpagkatpappvgpalgqhgvnimefckrfnaetadkagmilpvvitvyedksft
fiiktppasfllkkaagiekgssepkrkivgkvtrkqieeiaktkmpdlnansleaamki
iegtaksmgievv

  • Chain 'M':
    Sequence, based on SEQRES records: (download) 
    >1yl3M (M:)
msvaefdadvivdardcimgrvasqvaeqaldgetvavvnaeravitgreeqivekyekr
vdigndngyfypkrpdgifkrtirgmlphkkqrgreafesvrvylgnpydedgevldgts
ldrlsnikfvtlgeisetlganktw

    Sequence, based on observed residues (ATOM records): (download) 
    >1yl3M (M:)
aefdadvivdardcimgrvasqvaeqaldgetvavvnaeravitgreeqivekyekrvdi
gndngyfypkrpdgifkrtirgmlpkkqrgreafesvrvylgnpydtlgeisetlga

  • Chain 'N':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >1yl3N (N:)
miqqesrlkvadnsgarevlvikvlggsgrryanigdvvvatvkdatpggvvkkgqvvka
vvvrtkrgvrrpdgsyirfdenacviirddksprgtrifgpvarelrdkdfmkiislape
vi

  • Chain 'O':
    No sequence available.

  • Chain 'P':
    No sequence available.

  • Chain 'Q':
    No sequence available.

  • Chain 'R':
    Sequence, based on SEQRES records: (download) 
    >1yl3R (R:)
prtrecdycgtdiepgtgtmfvhkdgatthfcsskcennadlgrearnlewtdtargeag
eaedea

    Sequence, based on observed residues (ATOM records): (download) 
    >1yl3R (R:)
recdycgtdiepgtgtmfvhkdgatthfcsskcennadlrearnlewtdtar

  • Chain 'S':
    Sequence, based on SEQRES records: (download) 
    >1yl3S (S:)
meakaiaryvrisprkvrlvvdlirgksleearnilrytnkrgayfvakvlesaaanavn
nhdmledrlyvkaayvdegpalkrvlprargradiikkrtshitvilgekhgk

    Sequence, based on observed residues (ATOM records): (download) 
    >1yl3S (S:)
eakaiaryvrisprkvrlvvdlirgksleearnilrytnkrgayfvakvlesaaanavnn
hdledrlyvkaayvdegpalkrvlprargradiikkrtshitvilgek

  • Chain 'T':
    Sequence, based on SEQRES records: (download) 
    >1yl3T (T:)
swdvikhphvtekamndmdfqnklqfavddraskgevadaveeqydvtveqvntqntmdg
ekkavvrlsedddaqevasrigvf

    Sequence, based on observed residues (ATOM records): (download) 
    >1yl3T (T:)
swdvikhphvtekamndmdfnklqfavddraskgevadaveeqydvtveqvntqntmdge
kkavvrlsedddqeva

  • Chain 'U':
    Sequence, based on SEQRES records: (download) 
    >1yl3U (U:)
skqpdkqrksqrraplherhkqvratlsadlreeygqrnvrvnagdtvevlrgdfageeg
evinvdldkavihvedvtlektdgeevprpldtsnvrvtdldledekrearleseddsa

    Sequence, based on observed residues (ATOM records): (download) 
    >1yl3U (U:)
skqpdkqrksqrraplherhkqvratlsadlreeygvrvnagdtvevlrgdfageegevi
nvdldkavihvedvtlektdgeevprpldtsnvrvtdldledekrearle

  • Chain 'V':
    No sequence available.

  • Chain 'W':
    Sequence, based on SEQRES records: (download) 
    >1yl3W (W:)
tvlhvqeirdmtpaereaelddlktellnaravqaaggapenpgrikelrkaiariktiq
geegdlqene

    Sequence, based on observed residues (ATOM records): (download) 
    >1yl3W (W:)
tvlhvqeirdmtpaereaelddlktellnarvqaaggapenpgrikelrkaiariktiqg
eegd

  • Chain 'X':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >1yl3X (X:)
mprlkvklvkspigypkdqkaalkalglrrlqqervledtpairgnvekvahlvrvevve