PDB entry 6mss

View 6mss on RCSB PDB site
Description: Diversity in the type II Natural Killer T cell receptor repertoire and antigen specificity leads to differing CD1d docking strategies
Class: immune system
Keywords: NKT cells, CD1d molecule, microbial lipid antigen, IMMUNE SYSTEM
Deposited on 2018-10-18, released 2019-10-02
The last revision prior to the SCOPe 2.07 freeze date was dated 2019-10-02, with a file datestamp of 2019-09-27.
Experiment type: XRAY
Resolution: 3 Å
R-factor: N/A
AEROSPACI score: 0.13 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: A11B8.2 NKT TCR alpha-chain
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 6MSS
    Domains in SCOPe 2.07: d6mssa1, d6mssa2
  • Chain 'B':
    Compound: A11B8.2 NKT TCR beta-chain
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 6MSS (Start-244)
    Domains in SCOPe 2.07: d6mssb1, d6mssb2
  • Chain 'C':
    Compound: Antigen-presenting glycoprotein CD1d1
    Species: Mus musculus [TaxId:10090]
    Gene: Cd1d1, Cd1.1
    Database cross-references and differences (RAF-indexed):
    • Uniprot P11609 (Start-278)
      • expression tag (279)
    Domains in SCOPe 2.07: d6mssc1, d6mssc2, d6mssc3
  • Chain 'D':
    Compound: Beta-2-microglobulin
    Species: Mus musculus [TaxId:10090]
    Gene: B2M
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6mssd_
  • Heterogens: NAG, SRV, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >6mssA (A:)
mgmpveqnppalslyegadsglrcnfsttmksvqwfqqnhrgrlitlfylaqgtkengrl
kstfnskerystlhikdaqledsgtyfcaavnmgykltfgtgtsllvdpniqnpdpavyq
lrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavawsnksdf
acanafnnsiipedtffpspess

    Sequence, based on observed residues (ATOM records): (download) 
    >6mssA (A:)
mpveqnppalslyegadsglrcnfsttmksvqwfqqnhrgrlitlfylaqgtkengrlks
tfnskerystlhikdaqledsgtyfcaavnmgykltfgtgtsllvdpniqnpdpavyqlr
dsksksvclftdfdsqtnvsqssdvyitdkcvldmrsmdfksnsavawsnksdfacanaf
n

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >6mssB (B:)
meaavtqsprnkvavtggkvtlscnqtnnhnnmywyrqdtghglrlihysygagstekgd
ipdgykasrpsqenfslilelatpsqtsvyfcasgdpqgvsyeqyfgpgtrltvledlkn
vfppevavfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplke
qpalndsryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaea
wgrad

    Sequence, based on observed residues (ATOM records): (download) 
    >6mssB (B:)
vtqsprnkvavtggkvtlscnqtnnhnnmywyrqdtghglrlihysygagstekgdipdg
ykasrpsqenfslilelatpsqtsvyfcasgdpqgvsyeqyfgpgtrltvledlknvfpp
evavfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqpal
ndsryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawgra
d

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >6mssC (C:)
seaqqknytfrclqmssfanrswsrtdsvvwlgdlqthrwsndsatisftkpwsqgklsn
qqweklqhmfqvyrvsftrdiqelvkmmspkedypieiqlsagcemypgnasesflhvaf
qgkyvvrfwgtswqtvpgapswldlpikvlnadqgtsatvqmllndtcplfvrglleagk
sdlekqekpvawlssvpssahghrqlvchvsgfypkpvwvmwmrgdqeqqgthrgdflpn
adetwylqatldveageeaglacrvkhsslggqdiilywgslhhildaqkmvwnhrhhhh
hh

    Sequence, based on observed residues (ATOM records): (download) 
    >6mssC (C:)
nytfrclqmssfanrswsrtdsvvwlgdlqthrwsndsatisftkpwsqgklsnqqwekl
qhmfqvyrvsftrdiqelvkmmspkedypieiqlsagcemypgnasesflhvafqgkyvv
rfwgtswqtvpgapswldlpikvlnadqgtsatvqmllndtcplfvrglleagksdlekq
ekpvawlssvpghrqlvchvsgfypkpvwvmwmrgdqeqqgthrgdflpnadetwylqat
ldveageeaglacrvkhsslggqdiilywg

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

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