PDB entry 3vwk
View 3vwk on RCSB PDB site
Description: Ternary crystal structure of the human NKT TCR-CD1d-4'deoxy-alpha-galactosylceramide complex
Class: immune system
Keywords: cd1d, nkt t cell receptor, alpha-galactosylceramide, protein receptor complex, cell membrane, disulfide bond, endosome, glycoprotein, host-virus interaction, immune response, immunoglobulin domain, innate immunity, lysosome, membrane, transmembrane, disease mutation, glycation, MHC I, pyrrolidone carboxylic acid, secreted, immune system
Deposited on
2012-08-24, released
2012-10-03
The last revision prior to the SCOPe 2.08 freeze date was dated
2020-07-29, with a file datestamp of
2020-07-04.
Experiment type: XRAY
Resolution: 2.94 Å
R-factor: N/A
AEROSPACI score: 0.2
(click here for full SPACI score report)
Chains and heterogens:
- Chain 'A':
Compound: Antigen-presenting glycoprotein CD1d
Species: Homo sapiens [TaxId:9606]
Gene: CD1D
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.08: d3vwka1, d3vwka2 - Chain 'B':
Compound: Beta-2-microglobulin
Species: Homo sapiens [TaxId:9606]
Gene: B2M, CDABP0092, HDCMA22P
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.08: d3vwkb_ - Chain 'C':
Compound: NKT15 T cell receptor alpha-chain
Species: Homo sapiens [TaxId:9606]
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.08: d3vwkc1, d3vwkc2 - Chain 'D':
Compound: NKT15 T cell receptor beta-chain
Species: Homo sapiens [TaxId:9606]
Database cross-references and differences (RAF-indexed):
Domains in SCOPe 2.08: d3vwkd1, d3vwkd2 - Heterogens: NAG, 4GH, MG, HOH
PDB Chain Sequences:
- Chain 'A':
Sequence, based on SEQRES records: (download)
>3vwkA (A:)
spgvpqrlfplrclqissfansswtrtdglawlgelqthswsndsdtvrslkpwsqgtfs
dqqwetlqhifrvyrssftrdvkefakmlrlsyplelqvsagcevhpgnasnnffhvafq
gkdilsfqgtsweptqeaplwvnlaiqvlnqdkwtretvqwllngtcpqfvsgllesgks
elkkqvkpkawlsrgpspgpgrlllvchvsgfypkpvwvkwmrgeqeqqgtqpgdilpna
detwylratldvvageaaglscrvkhsslegqdivlywhhhhhh
Sequence, based on observed residues (ATOM records): (download)
>3vwkA (A:)
lfplrclqissfansswtrtdglawlgelqthswsndsdtvrslkpwsqgtfsdqqwetl
qhifrvyrssftrdvkefakmlrlsyplelqvsagcevhnnffhvafqgkdilsfqgtsw
eptqeaplwvnlaiqvlnqdkwtretvqwllngtcpqfvsgllesgkselkkqvkpkawl
srgpspgrlllvchvsgfypkpvwvkwmtqpgdilpnadetwylratldvlscrvkhssl
egqdivlyw
- Chain 'B':
Sequence, based on SEQRES records: (download)
>3vwkB (B:)
iqrtpkiqvysrhpaengksnflncyvsgfhpsdievdllkngeriekvehsdlsfskdw
sfyllyyteftptekdeyacrvnhvtlsqpkivkwdrdm
Sequence, based on observed residues (ATOM records): (download)
>3vwkB (B:)
qrtpkiqvysrhpaengksnflncyvsgfhpsdievdllkngeriekvehsdlsfskdws
fyllyyteftptekdeyacrvnhvtlsqpkivkwdr
- Chain 'C':
Sequence, based on SEQRES records: (download)
>3vwkC (C:)
mknqveqspqsliilegknctlqcnytvspfsnlrwykqdtgrgpvsltimtfsentksn
grytatldadtkqsslhitasqlsdsasyicvvsdrgstlgrlyfgrgtqltvwpdiqnp
dpavyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavaw
snksdfacanafnnsiipedtffpspess
Sequence, based on observed residues (ATOM records): (download)
>3vwkC (C:)
qveqspqsliilegknctlqcnytvspfsnlrwykqdtgrgpvsltimtfsentksngry
tatldadtkqsslhitasqlsdsasyicvvsdrgstlgrlyfgrgtqltvwpdiqnpdpa
vyqlrdssvclftdfdsqtnvsqsdsdvyitdkcvldmrsmdfksnsavawsnksdfaca
nafnnsiipedtff
- Chain 'D':
Sequence, based on SEQRES records: (download)
>3vwkD (D:)
meadiyqtprylvigtgkkitlecsqtmghdkmywyqqdpgmelhlihysygvnstekgd
lssestvsrirtehfpltlesarpshtsqylcassglrdrglyeqyfgpgtrltvtedlk
nvfppevavfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplk
eqpalndsryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsae
awgrad
Sequence, based on observed residues (ATOM records): (download)
>3vwkD (D:)
diyqtprylvigtgkkitlecsqtmghdkmywyqqdpgmelhlihysygvnstekgdlss
estvsrirtehfpltlesarpshtsqylcassglrdrglyeqyfgpgtrltvtedlknvf
ppevavfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqp
alndsryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawg
ra