PDB entry 5vcj
View 5vcj on RCSB PDB site
Description: Structure of alpha-galactosylphytosphingosine bound by CD1d and in complex with the Va14Vb8.2 TCR
Class: immune system
Keywords: immune system, antigen-presentation, TCR, MHC-fold
Deposited on
2017-03-31, released
2018-04-04
The last revision prior to the SCOPe 2.07 freeze date was dated
2018-04-04, with a file datestamp of
2018-03-29.
Experiment type: XRAY
Resolution: 3.16 Å
R-factor: N/A
AEROSPACI score: 0.12
(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):
Domains in SCOPe 2.07: d5vcja1, d5vcja2 - 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: d5vcjb_ - Chain 'C':
Compound: Chimeric TCR Valpha14/Jalpha18 chain (mouse variable domain, human constant domain)
Species: Homo sapiens [TaxId:9606]
Gene: B2M, HDCMA22P
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.07: d5vcjc1, d5vcjc2 - Chain 'D':
Compound: Chimeric TCR Vbeta8.2 chain (mouse variable domain, human constant domain)
Species: Homo sapiens [TaxId:9606]
Database cross-references and differences (RAF-indexed):
- PDB 5VCJ (Start-129)
- PDB 5VCJ (130-240)
Domains in SCOPe 2.07: d5vcjd1, d5vcjd2 - Heterogens: PBS, PLM, NAG, BMA, MAN, FUC
PDB Chain Sequences:
- Chain 'A':
Sequence, based on SEQRES records: (download)
>5vcjA (A:)
seaqqknytfrclqmssfanrswsrtdsvvwlgdlqthrwsndsatisftkpwsqgklsn
qqweklqhmfqvyrvsftrdiqelvkmmspkedypieiqlsagcemypgnasesflhvaf
qgkyvvrfwgtswqtvpgapswldlpikvlnadqgtsatvqmllndtcplfvrglleagk
sdlekqekpvawlssvpssahghrqlvchvsgfypkpvwvmwmrgdqeqqgthrgdflpn
adetwylqatldveageeaglacrvkhsslggqdiilywhhhhhh
Sequence, based on observed residues (ATOM records): (download)
>5vcjA (A:)
nytfrclqmssfanrswsrtdsvvwlgdlqthrwsndsatisftkpwsqgklsnqqwekl
qhmfqvyrvsftrdiqelvkmmspkedypieiqlsagcemypgnasesflhvafqgkyvv
rfwgtswqtvpgapswldlpikvlnadqgtsatvqmllndtcplfvrglleagksdlekq
ekpvawlssvhrqlvchvsgfypkpvwvmwmrgdqeqqgthrgdflpnadetwylqatld
veageeaglacrvkhsslggqdiilyw
- Chain 'B':
Sequence, based on SEQRES records: (download)
>5vcjB (B:)
iqktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdw
sfyilahteftptetdtyacrvkhasmaepktvywdrdm
Sequence, based on observed residues (ATOM records): (download)
>5vcjB (B:)
qktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdws
fyilahteftptetdtyacrvkhasmaepktvywdrdm
- Chain 'C':
Sequence, based on SEQRES records: (download)
>5vcjC (C:)
mktqveqspqslvvrqgencvlqcnysvtpdnhlrwfkqdtgkglvsltvlvdqkdktsn
grysatldkdakhstlhitatllddtatyicvvgdrgsalgrlhfgagtqlivipdiqnp
dpavyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavaw
snksdfacanafnnsiipedtffpspess
Sequence, based on observed residues (ATOM records): (download)
>5vcjC (C:)
tqveqspqslvvrqgencvlqcnysvtpdnhlrwfkqdtgkglvsltvlvdqkdktsngr
ysatldkdakhstlhitatllddtatyicvvgdrgsalgrlhfgagtqlivipdiqnpdp
avyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavawsn
kfacanafnnsiipedtffps
- Chain 'D':
Sequence, based on SEQRES records: (download)
>5vcjD (D:)
meaavtqsprnkvavtggkvtlscnqtnnhnnmywyrqdtghglrlihysygagstekgd
ipdgykasrpsqenfslilelatpsqtsvyfcasgdegytqyfgpgtrllvledlrnvtp
pkvslfepskaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqpa
lndsryslssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawgr
a
Sequence, based on observed residues (ATOM records): (download)
>5vcjD (D:)
aavtqsprnkvavtggkvtlscnqtnnhnnmywyrqdtghglrlihysygagstekgdip
dgykasrpsqenfslilelatpsqtsvyfcasgdegytqyfgpgtrllvledlrnvtppk
vslfepskaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqpaln
dsryslssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawgra