PDB entry 6omg

View 6omg on RCSB PDB site
Description: Structure of mouse CD1D- Glc-DAG (sn-1 C18:0, sn-2 C18:1c9)-iNKT TCR Ternary complex
Class: immune system
Keywords: glycolipid-antigen presentation, NKT cells, IMMUNE SYSTEM
Deposited on 2019-04-18, released 2020-04-22
The last revision prior to the SCOPe 2.08 freeze date was dated 2020-07-29, with a file datestamp of 2020-07-04.
Experiment type: XRAY
Resolution: 2.1 Å
R-factor: N/A
AEROSPACI score: 0.37 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Antigen-presenting glycoprotein CD1d1
    Species: Mus musculus [TaxId:10090]
    Gene: Cd1d1, mCG_3074
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6omga1, d6omga2
  • Chain 'B':
    Compound: Beta-2-microglobulin
    Species: Mus musculus [TaxId:10090]
    Gene: B2M
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6omgb_
  • Chain 'C':
    Compound: chimeric t cell antigen receptor alpha chain va14,va24
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 6OMG
    Domains in SCOPe 2.08: d6omgc1, d6omgc2
  • Chain 'D':
    Compound: Chimeric T cell antigen receptor beta chain Vb8.2, vb11
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 6OMG (Start-240)
    Domains in SCOPe 2.08: d6omgd1, d6omgd2
  • Heterogens: GOL, NA, MVV, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >6omgA (A:)
seaqqknytfrclqmssfanrswsrtdsvvwlgdlqthrwsndsatisftkpwsqgklsn
qqweklqhmfqvyrvsftrdiqelvkmmspkedypieiqlsagcemypgnasesflhvaf
qgkyvvrfwgtswqtvpgapswldlpikvlnadqgtsatvqmllndtcplfvrglleagk
sdlekqekpvawlssvpssahghrqlvchvsgfypkpvwvmwmrgdqeqqgthrgdflpn
adetwylqatldveageeaglacrvkhsslggqdiilywhhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >6omgA (A:)
knytfrclqmssfanrswsrtdsvvwlgdlqthrwsndsatisftkpwsqgklsnqqwek
lqhmfqvyrvsftrdiqelvkmmspkedypieiqlsagcemypgnasesflhvafqgkyv
vrfwgtswqtvpgapswldlpikvlnadqgtsatvqmllndtcplfvrglleagksdlek
qekpvawlssvpssahghrqlvchvsgfypkpvwvmwmrgdqeqqgthrgdflpnadetw
ylqatldveageeaglacrvkhsslggqdiilyw

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >6omgB (B:)
iqktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdw
sfyilahteftptetdtyacrvkhasmaepktvywdrdm

    Sequence, based on observed residues (ATOM records): (download) 
    >6omgB (B:)
ktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdwsf
yilahteftptetdtyacrvkhasmaepktvywdrdm

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >6omgC (C:)
mktqveqspqslvvrqgencvlqcnysvtpdnhlrwfkqdtgkglvsltvlvdqkdktsn
grysatldkdakhstlhitatllddtatyicvvgdrgsalgrlhfgagtqlivipdiqnp
dpavyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavaw
snksdfacanafnnsiipedtffpspess

    Sequence, based on observed residues (ATOM records): (download) 
    >6omgC (C:)
ktqveqspqslvvrqgencvlqcnysvtpdnhlrwfkqdtgkglvsltvlvdqkdktsng
rysatldkdakhstlhitatllddtatyicvvgdrgsalgrlhfgagtqlivipdiqnpd
pavyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavaws
nfacanafnnsiipedtffps

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >6omgD (D:)
meaavtqsprnkvavtggkvtlscnqtnnhnnmywyrqdtghglrlihysygagstekgd
ipdgykasrpsqenfslilelatpsqtsvyfcasgdegytqyfgpgtrllvledlrnvtp
pkvslfepskaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqpa
lndsryslssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawgr
a

    Sequence, based on observed residues (ATOM records): (download) 
    >6omgD (D:)
aavtqsprnkvavtggkvtlscnqtnnhnnmywyrqdtghglrlihysygagstekgdip
dgykasrpsqenfslilelatpsqtsvyfcasgdegytqyfgpgtrllvledlrnvtppk
vslfepskaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqpaln
dsryslssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawgra