PDB entry 4ei5

View 4ei5 on RCSB PDB site
Description: Crystal Structure of XV19 TCR in complex with CD1d-sulfatide C24:1
Class: immune system
Keywords: sulfatide, lipid, CD1d, NKT typeII, TCR, IMMUNE SYSTEM
Deposited on 2012-04-04, released 2012-07-25
The last revision prior to the SCOPe 2.05 freeze date was dated 2012-09-05, with a file datestamp of 2012-08-31.
Experiment type: XRAY
Resolution: 3.1 Å
R-factor: 0.199
AEROSPACI score: 0.24 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    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)
      • see remark 999 (200)
      • expression tag (279-300)
  • Chain 'B':
    Compound: Beta-2-microglobulin
    Species: Mus musculus [TaxId:10090]
    Gene: B2M
    Database cross-references and differences (RAF-indexed):
    • Uniprot P01887 (Start-98)
      • see remark 999 (84)
    Domains in SCOPe 2.05: d4ei5b_
  • Chain 'C':
    Compound: Valpha1 XV19 Type II Natural Killer T cell receptor (mouse variable domain, human constant domain)
    Species: Mus musculus, Homo sapiens [TaxId:10090, 9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 4EI5
    Domains in SCOPe 2.05: d4ei5c1, d4ei5c2
  • Chain 'D':
    Compound: Vbeta16 XV19 Type II Natural Killer T cell receptor (mouse variable domain, human constant domain)
    Species: Mus musculus, Homo sapiens [TaxId:10090, 9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 4EI5
    Domains in SCOPe 2.05: d4ei5d1, d4ei5d2
  • Chain 'E':
    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 (279-289)
    Domains in SCOPe 2.05: d4ei5e1, d4ei5e2
  • Chain 'F':
    Compound: Beta-2-microglobulin
    Species: Mus musculus [TaxId:10090]
    Gene: B2M
    Database cross-references and differences (RAF-indexed):
    • Uniprot P01887
      • see remark 999 (84)
    Domains in SCOPe 2.05: d4ei5f_
  • Chain 'G':
    Compound: Valpha1 XV19 Type II Natural Killer T cell receptor (mouse variable domain, human constant domain)
    Species: Mus musculus, Homo sapiens [TaxId:10090, 9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 4EI5
    Domains in SCOPe 2.05: d4ei5g1
  • Chain 'H':
    Compound: Vbeta16 XV19 Type II Natural Killer T cell receptor (mouse variable domain, human constant domain)
    Species: Mus musculus, Homo sapiens [TaxId:10090, 9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 4EI5
    Domains in SCOPe 2.05: d4ei5h1, d4ei5h2
  • Heterogens: NAG, FLC, CIS

PDB Chain Sequences:

  • Chain 'A':
    No sequence available.

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >4ei5B (B:)
iqktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdw
sfyilahteftptetdtyacrvkhasmaepktvywdrdm

    Sequence, based on observed residues (ATOM records): (download) 
    >4ei5B (B:)
qktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdws
fyilahteftptetdtyacrvkhasmaepktvywdrdm

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >4ei5C (C:)
mqqkvqqspeslsvpeggmaslnctssdrnfqyfwwyrqhsgegpkalmsifsdgdkkeg
rftahlnkaslhvslhirdsqpsdsalyfcaaseqnnyaqgltfglgtrvsvfpyiqnpd
pavyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavaws
nksdfacanafnnsiipedtffpspess

    Sequence, based on observed residues (ATOM records): (download) 
    >4ei5C (C:)
qkvqqspeslsvpeggmaslnctssdrnfqyfwwyrqhsgegpkalmsifsdgdkkegrf
tahlnkaslhvslhirdsqpsdsalyfcaaseqnnyaqgltfglgtrvsvfpyiqnpdpa
vyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavawsnk
sdfacanafnnsiipedtffp

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >4ei5D (D:)
mgpkvlqipshqiidmgqmvtlncdpvsnhlyfywykqilgqqmeflvnfyngkvmeksk
lfkdqfsverpdgsyftlkiqptaledsavyfcassfwgayaeqffgpgtrltvledlkn
vfppevavfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplke
qpalndsryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaea
wgrad

    Sequence, based on observed residues (ATOM records): (download) 
    >4ei5D (D:)
pkvlqipshqiidmgqmvtlncdpvsnhlyfywykqilgqqmeflvnfyngkvmeksklf
kdqfsverpdgsyftlkiqptaledsavyfcassfwgayaeqffgpgtrltvledlknvf
ppevavfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqp
alndsryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawg
ra

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >4ei5E (E:)
seaqqknytfrclqmssfanrswsrtdsvvwlgdlqthrwsndsatisftkpwsqgklsn
qqweklqhmfqvyrvsftrdiqelvkmmspkedypieiqlsagcemypgnasesflhvaf
qgkyvvrfwgtswqtvpgapswldlpikvlnadqgtsatvqmllndtcplfvrglleagk
sdlekqekpvawlssvpssahghrqlvchvsgfypkpvwvmwmrgdqeqqgthrgdflpn
adetwylqatldveageeaglacrvkhsslggqdiilywgslhhildaqkmvwnhrhhhh
hh

    Sequence, based on observed residues (ATOM records): (download) 
    >4ei5E (E:)
nytfrclqmssfanrswsrtdsvvwlgdlqthrwsndsatisftkpwsqgklsnqqwekl
qhmfqvyrvsftrdiqelvkmmspkedypieiqlsagcemypgnasesflhvafqgkyvv
rfwgtswqtvpgapswldlpikvlnadqgtsatvqmllndtcplfvrglleagksdlekq
ekpvawlssvpghrqlvchvsgfypkpvwvmwmrgdqeqqgthrgdflpnadetwylqat
ldveageeaglacrvkhsslggqdiilywgslhhildaqk

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >4ei5F (F:)
iqktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdw
sfyilahteftptetdtyacrvkhasmaepktvywdrdm

    Sequence, based on observed residues (ATOM records): (download) 
    >4ei5F (F:)
qktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdws
fyilahteftptetdtyacrvkhasmaepktvywd

  • Chain 'G':
    Sequence, based on SEQRES records: (download) 
    >4ei5G (G:)
mqqkvqqspeslsvpeggmaslnctssdrnfqyfwwyrqhsgegpkalmsifsdgdkkeg
rftahlnkaslhvslhirdsqpsdsalyfcaaseqnnyaqgltfglgtrvsvfpyiqnpd
pavyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavaws
nksdfacanafnnsiipedtffpspess

    Sequence, based on observed residues (ATOM records): (download) 
    >4ei5G (G:)
qkvqqspeslsvpeggmaslnctssdrnfqyfwwyrqhsgegpkalmsifsdgdkkegrf
tahlnkaslhvslhirdsqpsdsalyfcaaseqnnyaqgltfglgtrvsvfpyiqnpdpa
vyqlftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsnsiipedtffp

  • Chain 'H':
    Sequence, based on SEQRES records: (download) 
    >4ei5H (H:)
mgpkvlqipshqiidmgqmvtlncdpvsnhlyfywykqilgqqmeflvnfyngkvmeksk
lfkdqfsverpdgsyftlkiqptaledsavyfcassfwgayaeqffgpgtrltvledlkn
vfppevavfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplke
qpalndsryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaea
wgrad

    Sequence, based on observed residues (ATOM records): (download) 
    >4ei5H (H:)
gpkvlqipshqiidmgqmvtlncdpvsnhlyfywykqilgqqmeflvnfyngkvmekskl
fkdqfsverpdgsyftlkiqptaledsavyfcassfwgayaeqffgpgtrltvledlknv
fppevavfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqpndsr
yalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsa