PDB entry 3ubx

View 3ubx on RCSB PDB site
Description: Crystal structure of the mouse CD1d-C20:2-aGalCer-L363 mAb Fab complex
Class: immune system
Keywords: Immunology, mouse CD1d/NKT, mAb, IMMUNE SYSTEM
Deposited on 2011-10-25, released 2011-11-16
The last revision prior to the SCOPe 2.06 freeze date was dated 2013-08-28, with a file datestamp of 2013-08-23.
Experiment type: XRAY
Resolution: 3.1 Å
R-factor: 0.203
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: Cd1.1, CD1d, Cd1d1
    Database cross-references and differences (RAF-indexed):
    • Uniprot P11609 (Start-278)
      • expression tag (279-285)
    Domains in SCOPe 2.06: d3ubxa1, d3ubxa2, d3ubxa3
  • Chain 'B':
    Compound: Beta-2-microglobulin
    Species: Mus musculus [TaxId:10090]
    Gene: B2m, CD1d
    Database cross-references and differences (RAF-indexed):
    • Uniprot P01887 (0-98)
      • see remark 999 (84)
    Domains in SCOPe 2.06: d3ubxb_
  • Chain 'D':
    Compound: Antigen-presenting glycoprotein CD1d1
    Species: Mus musculus [TaxId:10090]
    Gene: Cd1.1, CD1d, Cd1d1
    Database cross-references and differences (RAF-indexed):
    • Uniprot P11609 (Start-278)
      • expression tag (279-285)
    Domains in SCOPe 2.06: d3ubxd1, d3ubxd2, d3ubxd3
  • Chain 'E':
    Compound: Beta-2-microglobulin
    Species: Mus musculus [TaxId:10090]
    Gene: B2m, CD1d
    Database cross-references and differences (RAF-indexed):
    • Uniprot P01887 (Start-98)
      • see remark 999 (84)
    Domains in SCOPe 2.06: d3ubxe_
  • Chain 'G':
    Compound: L363 heavy chain (IGHV9-4*02)
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 3UBX (0-221)
  • Chain 'H':
    Compound: L363 heavy chain (IGHV9-4*02)
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 3UBX (0-221)
  • Chain 'I':
    Compound: L363 light chain (IGKV13-84*01)
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 3UBX (0-213)
    Domains in SCOPe 2.06: d3ubxi1, d3ubxi2
  • Chain 'L':
    Compound: L363 light chain (IGKV13-84*01)
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 3UBX (0-213)
    Domains in SCOPe 2.06: d3ubxl1, d3ubxl2
  • Heterogens: 09N, NAG

PDB Chain Sequences:

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

    Sequence, based on observed residues (ATOM records): (download) 
    >3ubxA (A:)
knytfrclqmssfanrswsrtdsvvwlgdlqthrwsndsatisftkpwsqgklsnqqwek
lqhmfqvyrvsftrdiqelvkmmspkedypieiqlsagcemypgnasesflhvafqgkyv
vrfwgtswqtvpgapswldlpikvlnadqgtsatvqmllndtcplfvrglleagksdlek
qekpvawlssghrqlvchvsgfypkpvwvmwmrgdqeqqgthrgdflpnadetwylqatl
dveageeaglacrvkhsslggqdiilywhhhhhhh

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

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >3ubxD (D:)
seaqqknytfrclqmssfanrswsrtdsvvwlgdlqthrwsndsatisftkpwsqgklsn
qqweklqhmfqvyrvsftrdiqelvkmmspkedypieiqlsagcemypgnasesflhvaf
qgkyvvrfwgtswqtvpgapswldlpikvlnadqgtsatvqmllndtcplfvrglleagk
sdlekqekpvawlssvpssahghrqlvchvsgfypkpvwvmwmrgdqeqqgthrgdflpn
adetwylqatldveageeaglacrvkhsslggqdiilywhhhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >3ubxD (D:)
knytfrclqmssfanrswsrtdsvvwlgdlqthrwsndsatisftkpwsqgklsnqqwek
lqhmfqvyrvsftrdiqelvkmmspkedypieiqlsagcemypgnasesflhvafqgkyv
vrfwgtswqtvpgapswldlpikvlnadqgtsatvqmllndtcplfvrglleagksdlek
qekpvawlssvghrqlvchvsgfypkpvwvmwmrgdqeqqgthrgdflpnadetwylqat
ldveageeaglacrvkhsslggqdiilywhhhhhhh

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >3ubxE (E:)
iqktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdw
sfyilahteftptetdtyacrvkhasmaepktvywdrdm

    Sequence, based on observed residues (ATOM records): (download) 
    >3ubxE (E:)
qktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdws
fyilahteftptetdtyacrvkhasmaepktvywdrdm

  • Chain 'G':
    No sequence available.

  • Chain 'H':
    No sequence available.

  • Chain 'I':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >3ubxI (I:)
diqmtqssssfsvslgdratitckasediynriawyqqkpgnvprllisgatsletgvps
rfsgsgsgkdytlsitslqtedvatyycqhywsspltfgagtklelkradaaptvsifpp
sseqltsggasvvcflnnfypkdinvkwkidgserqngvlnswtdqdskdstysmsstlt
ltkdeyerhnsytceathktstspivksfnrnec

  • Chain 'L':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >3ubxL (L:)
diqmtqssssfsvslgdratitckasediynriawyqqkpgnvprllisgatsletgvps
rfsgsgsgkdytlsitslqtedvatyycqhywsspltfgagtklelkradaaptvsifpp
sseqltsggasvvcflnnfypkdinvkwkidgserqngvlnswtdqdskdstysmsstlt
ltkdeyerhnsytceathktstspivksfnrnec