PDB entry 1vsp

View 1vsp on RCSB PDB site
Description: Interactions and Dynamics of the Shine-Dalgarno Helix in the 70S Ribosome. This file, 1VSP, contains the 50S ribosome subunit. 30S ribosome subunit is in the file 2QNH
Class: ribosome
Keywords: 70S ribosome, Shine-Dalgarno, RIBOSOME
Deposited on 2007-07-18, released 2007-11-13
The last revision prior to the SCOPe 2.08 freeze date was dated 2014-12-10, with a file datestamp of 2014-12-05.
Experiment type: XRAY
Resolution: 3.83 Å
R-factor: 0.327
AEROSPACI score: -0.06 (click here for full SPACI score report)

Chains and heterogens:

• Chain 'A':
  Compound: 50s ribosomal protein l1
  Species: Thermus thermophilus [TaxId:262724]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q72GV9 (Start-228)
  Domains in SCOPe 2.08: d1vspa1
• Chain 'B':
  Compound: 50S ribosomal protein L2
  Species: Thermus thermophilus [TaxId:262724]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q72I07
• Chain 'C':
  Compound: 50S ribosomal protein L3
  Species: Thermus thermophilus [TaxId:262724]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q72I04
  Domains in SCOPe 2.08: d1vspc1
• Chain 'D':
  Compound: 50S ribosomal protein L4
  Species: Thermus thermophilus [TaxId:262724]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q72I05
• Chain 'E':
  Compound: 50S ribosomal protein L5
  Species: Thermus thermophilus [TaxId:262724]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q72I16 (Start-181)
• Chain 'F':
  Compound: 50S ribosomal protein L6
  Species: Thermus thermophilus [TaxId:262724]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q72I19
  Domains in SCOPe 2.08: d1vspf1, d1vspf2
• Chain 'G':
  Compound: 50S ribosomal protein L9
  Species: Thermus thermophilus [TaxId:262724]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q72GV5 (0-147)
• Chain 'H':
  Compound: 50S ribosomal protein L13
  Species: Thermus thermophilus [TaxId:262724]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q72IN1 (0-End)
    • conflict (0)
• Chain 'I':
  Compound: 50S ribosomal protein L14
  Species: Thermus thermophilus [TaxId:262724]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q72I14 (0-121)
  Domains in SCOPe 2.08: d1vspi1
• Chain 'J':
  Compound: 50S ribosomal protein L15
  Species: Thermus thermophilus [TaxId:262724]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q72I23 (Start-149)
  Domains in SCOPe 2.08: d1vspj1
• Chain 'K':
  Compound: 50S ribosomal protein L16
  Species: Thermus thermophilus [TaxId:262724]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q72I11 (0-End)
• Chain 'L':
  Compound: 50S ribosomal protein L17
  Species: Thermus thermophilus [TaxId:262724]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q72I33 (0-117)
• Chain 'M':
  Compound: 50S ribosomal protein L18
  Species: Thermus thermophilus [TaxId:262724]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q72I20 (Start-111)
• Chain 'N':
  Compound: 50S ribosomal protein L19
  Species: Thermus thermophilus [TaxId:262724]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q72JU9 (0-End)
• Chain 'O':
  Compound: 50S ribosomal protein L20
  Species: Thermus thermophilus [TaxId:262724]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q72L76 (Start-117)
  Domains in SCOPe 2.08: d1vspo1
• Chain 'P':
  Compound: 50S ribosomal protein L21
  Species: Thermus thermophilus [TaxId:262724]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q72HR2 (0-100)
  Domains in SCOPe 2.08: d1vspp1
• Chain 'Q':
  Compound: 50S ribosomal protein L22
  Species: Thermus thermophilus [TaxId:262724]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q72I09
• Chain 'R':
  Compound: 50S ribosomal protein L23
  Species: Thermus thermophilus [TaxId:262724]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q72I06
• Chain 'S':
  Compound: 50S ribosomal protein L24
  Species: Thermus thermophilus [TaxId:262724]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q72I15 (0-End)
  Domains in SCOPe 2.08: d1vsps1
• Chain 'T':
  Compound: 50S ribosomal protein L25
  Species: Thermus thermophilus [TaxId:262724]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q72IA7 (0-End)
  Domains in SCOPe 2.08: d1vspt1
• Chain 'U':
  Compound: 50S ribosomal protein L27
  Species: Thermus thermophilus [TaxId:262724]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q72HR3 (Start-84)
• Chain 'V':
  Compound: LSU ribosomal protein L28P
  Species: Thermus thermophilus [TaxId:262724]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q72G84
• Chain 'W':
  Compound: 50S ribosomal protein L29
  Species: Thermus thermophilus [TaxId:262724]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q72I12 (0-End)
• Chain 'X':
  Compound: LSU ribosomal protein L30P
  Species: Thermus thermophilus [TaxId:262724]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q72I22 (0-59)
• Chain 'Y':
  Compound: 50S ribosomal protein L32
  Species: Thermus thermophilus [TaxId:262724]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P62652 (Start-59)
• Chain 'Z':
  Compound: 50S ribosomal protein L34
  Species: Thermus thermophilus [TaxId:262724]
  Database cross-references and differences (RAF-indexed):
  • Uniprot P80340 (0-End)
  Domains in SCOPe 2.08: d1vspz1
• Chain 'a':
  Compound: 50S ribosomal protein L35
  Species: Thermus thermophilus [TaxId:262724]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q72L77
• Chain 'b':
  Compound: 50S ribosomal protein L36
  Species: Thermus thermophilus [TaxId:262724]
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q72I28
• Chain 'w':
  Compound: 23s large subunit ribosomal RNA
  Species: Thermus thermophilus [TaxId:262724]
  
• Chain 'x':
  Compound: 5s large subunit ribosomal RNA
  Species: Thermus thermophilus [TaxId:262724]
  

PDB Chain Sequences:

• Chain 'A':
  Sequence, based on SEQRES records: (download)
  

  >1vspA (A:)
  mpkhgkryrallekvdpnkiytideaahlvkelatakfdetvevhaklgidprrsdqnvr
  gtvslphglgkqvrvlaiakgekikeaeeagadyvggeeiiqkildgwmdfdavvatpdv
  mgavgsklgrilgprgllpnpkagtvgfnigeiireikagriefrndktgaihapvgkas
  fppekladnirafiraleahkpegakgtflrsvyvtttmgpsvrinphs
  

  
  Sequence, based on observed residues (ATOM records): (download)
  

  >1vspA (A:)
  kryrallekvdpnkiytideaahlvkelatakfdetvevhaklgidprrsdqnvrgtvsi
  efrndktgaihapvgkasfppekladnirafiraleahkpegakgtflrsvyvtttmgps
  vrinphs
  

  
  
• Chain 'B':
  No sequence available.
  
  
• Chain 'C':
  Sequence, based on SEQRES records: (download)
  

  >1vspC (C:)
  mkgilgvkvgmtrifrddravpvtvilagpcpvvqrrtpekdgytavqlgflpqnpkrvn
  rplkghfakagvepvrilreirdfnpegdtvtveifkpgervdvtgtskgrgfagvmkrw
  nfaggpdshgahkihrhpgsignrktpgrvykgkkmaghygaervtvmnlevvdvipeen
  lllvkgavpgpngglvivretkkaak
  

  
  Sequence, based on observed residues (ATOM records): (download)
  

  >1vspC (C:)
  gilgvkvgmtrifrddravpvtvilagpcpvvqrrtpekdgytavqlgflpqnpkrvnrp
  lkghfakagvepvrilreirdfnpegdtvtveifkpgervdvtgtskgrgfagvmkrwnf
  aggpdshgahkihrhpgsignrktpgrvykgkkmaghygaervtvmnlevvdvipeenll
  lvkgavpgpngglvivretkk
  

  
  
• Chain 'D':
  No sequence available.
  
  
• Chain 'E':
  No sequence available.
  
  
• Chain 'F':
  Sequence, based on SEQRES records: (download)
  

  >1vspF (F:)
  msrigrlpipvpkgvsvevapgrvkvkgpkgelevpvspemrvvveegvvrverpsderr
  hkslhgltrtlianavkgvsegyskellikgigyrarlvgraleltvgfshpvvveppeg
  itfevpeptrvrvsgidkqkvgqvaanirairkpsayhekgiyyagepvrlkpgkagakk
  

  
  Sequence, based on observed residues (ATOM records): (download)
  

  >1vspF (F:)
  lpipvpkgvsvevapgrvkvkgpkgelevpvspemrvvveegvvrverpsderrhkslhg
  ltrtlianavkgvsegyskellikgigyrarlvgraleltvgfshpvvveppegitfevp
  eptrvrvsgidkqkvgqvaanirairkpsayhekgiyyagepvrlkpgkagak
  

  
  
• Chain 'G':
  No sequence available.
  
  
• Chain 'H':
  No sequence available.
  
  
• Chain 'I':
  Sequence; same for both SEQRES and ATOM records: (download)
  

  >1vspI (I:)
  miqpqtylevadntgarkimcirvlkgsnakyatvgdvivasvkeaiprgavkegdvvka
  vvvrtkkevkrpdgsairfddnaaviinnqleprgtrvfgpvarelrekgfmkivslape
  vl
  

  
  
• Chain 'J':
  Sequence, based on SEQRES records: (download)
  

  >1vspJ (J:)
  mklsdlrpnpgankrrkrvgrgpgsghgktatrghkgqksrsgglkdprrfeggrsttlm
  rlpkrgmqgqvpgeikrpryqgvnlkdlarfegevtpellvragllkkgyrlkilgegea
  kplkvvahafsksaleklkaaggepvllea
  

  
  Sequence, based on observed residues (ATOM records): (download)
  

  >1vspJ (J:)
  dlrpnpgankrrkrvgrgpgsghgktatrghkgqksrsgglkdprrfeggrsttlmrlpk
  rgmqgqvpgeikrpryqgvnlkdlarfegevtpellvragllkkgyrlkilgegeakplk
  vvahafsksaleklkaaggepvllea
  

  
  
• Chain 'K':
  No sequence available.
  
  
• Chain 'L':
  No sequence available.
  
  
• Chain 'M':
  No sequence available.
  
  
• Chain 'N':
  No sequence available.
  
  
• Chain 'O':
  Sequence, based on SEQRES records: (download)
  

  >1vspO (O:)
  mpraktgvvrrrkhkkilklakgywglrsksfrkaretlfaagnyayahrkrrkrdfrrl
  wivrinaacrqhglnystfihglkkagievdrknladlavrepqvfaelverakaaqg
  

  
  Sequence, based on observed residues (ATOM records): (download)
  

  >1vspO (O:)
  praktgvvrrrkhkkilklakgywglrsksfrkaretlfaagnyayahrkrrkrdfrrlw
  ivrinaacrqhglnystfihglkkagievdrknladlavrepqvfaelverakaaqg
  

  
  
• Chain 'P':
  Sequence; same for both SEQRES and ATOM records: (download)
  

  >1vspP (P:)
  mfaivktggkqyrvepglklrvekldaepgatvelpvlllggektvvgtpvvegasvvae
  vlghgrgkkilvskfkakvqyrrkkghrqpytellikeirg
  

  
  
• Chain 'Q':
  No sequence available.
  
  
• Chain 'R':
  No sequence available.
  
  
• Chain 'S':
  Sequence, based on SEQRES records: (download)
  

  >1vspS (S:)
  mrvkmhvkkgdtvlvasgkykgrvgkvkevlpkkyavivegvnivkkavrvspkypqggf
  iekeaplhaskvrpicpacgkptrvrkkflengkkirvcakcggaldtee
  

  
  Sequence, based on observed residues (ATOM records): (download)
  

  >1vspS (S:)
  mrvkmhvkkgdtvlvasgkykgrvgkvkevlpkkyavivegvnivkkavrvspkypqggf
  iekeaplhaskvrpicpacgkptrvrkkflengkkirvcakcg
  

  
  
• Chain 'T':
  Sequence, based on SEQRES records: (download)
  

  >1vspT (T:)
  meyrlkayyregekpsalrragklpgvmynrhlnrkvyvdlvefdkvfrqasihhvivle
  lpdgqslptlvrqvnldkrrrrpehvdffvlsdepvemyvplrfvgtpagvraggvlqei
  hrdilvkvsprnipefievdvsgleigdslhasdlklppgvelavspeetiaavvppedv
  eklaeeaaaevaepevikkgkeeeee
  

  
  Sequence, based on observed residues (ATOM records): (download)
  

  >1vspT (T:)
  meyrlkayyregekpsalrragklpgvmynrhlnrkvyvdlvefdkvfrqasihhvivle
  lpdgqslptlvrqvnldkrrrrpehvdffvlsdepvemyvplrfvgtpagvraggvlqei
  hrdilvkvsprnipefievdvsgleigdslhasdlklppgvelavspeetiaavvppedv
  eklae
  

  
  
• Chain 'U':
  No sequence available.
  
  
• Chain 'V':
  No sequence available.
  
  
• Chain 'W':
  No sequence available.
  
  
• Chain 'X':
  No sequence available.
  
  
• Chain 'Y':
  No sequence available.
  
  
• Chain 'Z':
  Sequence, based on SEQRES records: (download)
  

  >1vspZ (Z:)
  mkrtwqpnrrkrakthgfrarmrtpggrkvlkrrrqkgrwrltpavrkr
  

  
  Sequence, based on observed residues (ATOM records): (download)
  

  >1vspZ (Z:)
  mkrtwqpnrrkrakthgfrarmrtpggrkvlkrrrqkgrwrltpavrk
  

  
  
• Chain 'a':
  No sequence available.
  
  
• Chain 'b':
  No sequence available.
  
  
• Chain 'w':
  No sequence available.
  
  
• Chain 'x':
  No sequence available.