PDB entry 3sda

View 3sda on RCSB PDB site
Description: Crystal structure of autoreactive-Valpha14-Vbeta6 NKT TCR in complex with CD1d-beta-galactosylceramide
Class: immune system
Keywords: CD1d, beta-linked antigen, Immunity, NKT, autoreactive, IMMUNE SYSTEM
Deposited on 2011-06-08, released 2011-10-05
The last revision prior to the SCOPe 2.03 freeze date was dated 2011-10-05, with a file datestamp of 2011-09-30.
Experiment type: XRAY
Resolution: 2.8 Å
R-factor: 0.274
AEROSPACI score: 0.19 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Antigen-presenting glycoprotein CD1d1
    Species: Mus musculus [TaxId:10090]
    Gene: Cd1.1, Cd1d1
    Database cross-references and differences (RAF-indexed):
    • Uniprot P11609 (Start-278)
      • see remark 999 (200)
      • expression tag (279-294)
    Domains in SCOPe 2.03: d3sdaa1, d3sdaa2
  • Chain 'B':
    Compound: Beta-2-microglobulin
    Species: Mus musculus [TaxId:10090]
    Gene: B2M
    Database cross-references and differences (RAF-indexed):
    • Uniprot P01887 (0-98)
      • see remark 999 (84)
    Domains in SCOPe 2.03: d3sdab_
  • Chain 'C':
    Compound: NKT TCR Valpha14 chain
    Species: Mus musculus , Homo sapiens [TaxId:10090, 9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 3SDA (0-End)
    Domains in SCOPe 2.03: d3sdac1, d3sdac2
  • Chain 'D':
    Compound: NKT TCR autoreactive-Vbeta6 chain
    Species: Mus musculus , Homo sapiens [TaxId:10090, 9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 3SDA
    Domains in SCOPe 2.03: d3sdad1, d3sdad2
  • Heterogens: NAG, GCY, GOL, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >3sdaA (A:)
seaqqknytfrclqmssfanrswsrtdsvvwlgdlqthrwsndsatisftkpwsqgklsn
qqweklqhmfqvyrvsftrdiqelvkmmspkedypieiqlsagcemypgnasesflhvaf
qgkyvvrfwgtswqtvpgapswldlpikvlnadqgtsatvqmllndtcplfvrglleagk
sdlekqekpvawlssvpssahghrqlvchvsgfypkpvwvmwmrgdqeqqgthrgdflpn
adetwylqatldveageeaglacrvkhsslggqdiilywgslhhildaqkmvwnhrhhhh
hh

    Sequence, based on observed residues (ATOM records): (download) 
    >3sdaA (A:)
knytfrclqmssfanrswsrtdsvvwlgdlqthrwsndsatisftkpwsqgklsnqqwek
lqhmfqvyrvsftrdiqelvkmmspkedypieiqlsagcemypgnasesflhvafqgkyv
vrfwgtswqtvpgapswldlpikvlnadqgtsatvqmllndtcplfvrglleagksdlek
qekpvawlssvpssahghrqlvchvsgfypkpvwvmwmrgdqeqqgthrgdflpnadetw
ylqatldveageeaglacrvkhsslggqdiilywgslhhildaqkmvwnh

  • Chain 'B':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >3sdaB (B:)
iqktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdw
sfyilahteftptetdtyacrvkhasmaepktvywdrdm

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >3sdaC (C:)
tqveqspqslvvrqgensvlqcnysvtpdnhlrwfkqdtgkglvsltvlvdqkdktsngr
ysatldkdakhstlhitatllddtatyicvvgdrgsalgrlhfgagtqlivipdiqnpdp
avyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavawsn
ksdfacanafnnsiipedtffpspess

    Sequence, based on observed residues (ATOM records): (download) 
    >3sdaC (C:)
tqveqspqslvvrqgensvlqcnysvtpdnhlrwfkqdtgkglvsltvlvdqkdktsngr
ysatldkdakhstlhitatllddtatyicvvgdrgsalgrlhfgagtqlivipdiqnpdp
avyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavawsa
canafnnsiipedtff

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >3sdaD (D:)
hmggiitqtpkfligqegqkltlkcqqnfnhdtmywyrqdsgkglrliyysygagstekg
dlsegydasrekkssfsltvtsaqknemavflcasgslldvrevffgkgtrltvvedlkn
vfppevavfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplke
qpalndsryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaea
wgrad

    Sequence, based on observed residues (ATOM records): (download) 
    >3sdaD (D:)
ggiitqtpkfligqegqkltlkcqqnfnhdtmywyrqdsgkglrliyysygagstekgdl
segydasrekkssfsltvtsaqknemavflcasgslldvrevffgkgtrltvvedlknvf
ppevavfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqp
alndsryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeaw