PDB entry 6mj4

View 6mj4 on RCSB PDB site
Description: Crystal structure of MCD1D/INKTCR TERNARY COMPLEX bound to glycolipid (XXW)
Class: immune system
Keywords: MHC-fold, Ig-fold, glycolipid antigen presentation, T cell receptor, IMMUNE SYSTEM
Deposited on 2018-09-20, released 2019-01-09
The last revision prior to the SCOPe 2.07 freeze date was dated 2019-01-16, with a file datestamp of 2019-01-11.
Experiment type: XRAY
Resolution: 2 Å
R-factor: N/A
AEROSPACI score: 0.31 (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 2.07: d6mj4a1, d6mj4a2
  • Chain 'B':
    Compound: Beta-2-microglobulin
    Species: Mus musculus [TaxId:10090]
    Gene: B2M
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6mj4b_
  • Chain 'C':
    Compound: T cell receptor alpha variable 11,T cell receptor alpha variable 11,T cell receptor alpha joining 18,Human nkt tcr alpha chain, CHIMERIC PROTEIN
    Species: Homo sapiens [TaxId:9606]
    Gene: B2M, HDCMA22P
    Database cross-references and differences (RAF-indexed):
    • Uniprot A0A0B4J1J9 (1-92)
      • linker (113)
    • PDB 6MJ4 (93-112)
    • Uniprot K7N5M3 (114-End)
    Domains in SCOPe 2.07: d6mj4c1, d6mj4c2
  • Chain 'D':
    Compound: Beta-chain,T cell receptor chain,T cell receptor beta constant 2, CHIMERIC PROTEIN
    Species: Homo sapiens [TaxId:9606]
    Gene: TRBC2, TCRBC2
    Database cross-references and differences (RAF-indexed):
    • Uniprot A2NTY6 (Start-94)
      • linker (95-98)
    • Uniprot A0N8J3 (99-130)
      • linker (130)
    • Uniprot A0A5B9 (131-240)
      • variant (168)
      • variant (186)
    Domains in SCOPe 2.07: d6mj4d1, d6mj4d2
  • Heterogens: GOL, NA, NAG, FUC, JTG, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >6mj4A (A:)
seaqqknytfrclqmssfanrswsrtdsvvwlgdlqthrwsndsatisftkpwsqgklsn
qqweklqhmfqvyrvsftrdiqelvkmmspkedypieiqlsagcemypgnasesflhvaf
qgkyvvrfwgtswqtvpgapswldlpikvlnadqgtsatvqmllndtcplfvrglleagk
sdlekqekpvawlssvpssahghrqlvchvsgfypkpvwvmwmrgdqeqqgthrgdflpn
adetwylqatldveageeaglacrvkhsslggqdiilywhhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >6mj4A (A:)
nytfrclqmssfanrswsrtdsvvwlgdlqthrwsndsatisftkpwsqgklsnqqwekl
qhmfqvyrvsftrdiqelvkmmspkedypieiqlsagcemypgnasesflhvafqgkyvv
rfwgtswqtvpgapswldlpikvlnadqgtsatvqmllndtcplfvrglleagksdlekq
ekpvawlssvpssahghrqlvchvsgfypkpvwvmwmrgdqeqqgthrgdflpnadetwy
lqatldveageeaglacrvkhsslggqdiilyw

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >6mj4B (B:)
iqktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdw
sfyilahteftptetdtyacrvkhasmaepktvywdrdm

    Sequence, based on observed residues (ATOM records): (download) 
    >6mj4B (B:)
qktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdws
fyilahteftptetdtyacrvkhasmaepktvywdrdm

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >6mj4C (C:)
mktqveqspqslvvrqgencvlqcnysvtpdnhlrwfkqdtgkglvsltvlvdqkdktsn
grysatldkdakhstlhitatllddtatyicvvgdrgsalgrlhfgagtqlivipdiqnp
dpavyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavaw
snksdfacanafnnsiipedtffpspess

    Sequence, based on observed residues (ATOM records): (download) 
    >6mj4C (C:)
ktqveqspqslvvrqgencvlqcnysvtpdnhlrwfkqdtgkglvsltvlvdqkdktsng
rysatldkdakhstlhitatllddtatyicvvgdrgsalgrlhfgagtqlivipdiqnpd
pavyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavaws
nfacanafnnsiipedtffps

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >6mj4D (D:)
meaavtqsprnkvavtggkvtlscnqtnnhnnmywyrqdtghglrlihysygagstekgd
ipdgykasrpsqenfslilelatpsqtsvyfcasgdegytqyfgpgtrllvledlrnvtp
pkvslfepskaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqpa
lndsryslssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawgr
a

    Sequence, based on observed residues (ATOM records): (download) 
    >6mj4D (D:)
aavtqsprnkvavtggkvtlscnqtnnhnnmywyrqdtghglrlihysygagstekgdip
dgykasrpsqenfslilelatpsqtsvyfcasgdegytqyfgpgtrllvledlrnvtppk
vslfepskaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqpaln
dsryslssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawgra