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Protein Structures and Oligomeric States

Enter a protein name, UniProt accession or PDB ID. Name searches ask you to confirm the protein identity before related structures are queried.

Current Protein Identity：P15813 New Search
22PDB entries
32Biological assembly
34chain/assembly records
Main Difference Dimensions in This Set
Different construct Different mutation/modification Different assembly state Different ligand/ion Different experimental conditions Different structure-quality metrics

Difference tags compare only the current result set; every original PDB and assembly record remains separate.

Related-Structure Differences

Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method Experimental Conditions Structure Quality
1ZT4 The crystal structure of human CD1d with and without alpha-Galactosylceramide Deposited 2005-05-26 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 19–300（282 aa） Fragment：CD1d heavy chain
Not recorded AGH N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；PEG3350, potassium fluoride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Resolution 3.00 Å R-free 0.326
1ZT4 The crystal structure of human CD1d with and without alpha-Galactosylceramide Deposited 2005-05-26 Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain C 19–300（282 aa） Fragment：CD1d heavy chain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；PEG3350, potassium fluoride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Resolution 3.00 Å R-free 0.326
1ZT4 The crystal structure of human CD1d with and without alpha-Galactosylceramide Deposited 2005-05-26 Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain A 19–300（282 aa） Fragment：CD1d heavy chain
Chain C 19–300（282 aa） Fragment：CD1d heavy chain
Not recorded AGH N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；PEG3350, potassium fluoride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Resolution 3.00 Å R-free 0.326
2PO6 Crystal structure of CD1d-lipid-antigen complexed with Beta-2-Microglobulin, NKT15 Alpha-Chain and NKT15 Beta-Chain Deposited 2007-04-25 Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain A 24–295（272 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 AGH N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；13% PEG 10K, 0.1M bis-tris propane, 0.2M tri-sodium citrate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.20 Å R-free 0.293
2PO6 Crystal structure of CD1d-lipid-antigen complexed with Beta-2-Microglobulin, NKT15 Alpha-Chain and NKT15 Beta-Chain Deposited 2007-04-25 Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain E 24–295（272 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 AGH N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；13% PEG 10K, 0.1M bis-tris propane, 0.2M tri-sodium citrate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.20 Å R-free 0.293
3HUJ Crystal structure of human CD1d-alpha-Galactosylceramide in complex with semi-invariant NKT cell receptor Deposited 2009-06-14 Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain A 21–295（275 aa） Fragment：UNP residues 21-295
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 AGH N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；291 K；0.1M Tris-HCl, 0.2M magnesium chloride, 12% PEG 10000, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.50 Å R-free 0.279
3HUJ Crystal structure of human CD1d-alpha-Galactosylceramide in complex with semi-invariant NKT cell receptor Deposited 2009-06-14 Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain C 21–295（275 aa） Fragment：UNP residues 21-295
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 AGH N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；291 K；0.1M Tris-HCl, 0.2M magnesium chloride, 12% PEG 10000, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.50 Å R-free 0.279
3SDX Crystal structure of human autoreactive-Valpha24 NKT TCR in complex with CD1d-beta-galactosylceramide Deposited 2011-06-09 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain A 24–295（272 aa） Fragment：extracellular domain, UNP residues 24-295
Not recorded GCY N-[(2S,3R)-1-(beta-D-galactopyranosyloxy)-3-hydroxyoctadec-4-en-2-yl]tetracosanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；30% PEG 400, 0.1M Tris, 0.1M MgCl2, pH 8.5, vapor diffusion, hanging drop, temperature 293K
Resolution 3.12 Å R-free 0.273
3SDX Crystal structure of human autoreactive-Valpha24 NKT TCR in complex with CD1d-beta-galactosylceramide Deposited 2011-06-09 Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain C 24–295（272 aa） Fragment：extracellular domain, UNP residues 24-295
Not recorded GCY N-[(2S,3R)-1-(beta-D-galactopyranosyloxy)-3-hydroxyoctadec-4-en-2-yl]tetracosanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；30% PEG 400, 0.1M Tris, 0.1M MgCl2, pH 8.5, vapor diffusion, hanging drop, temperature 293K
Resolution 3.12 Å R-free 0.273
3TZV Crystal structure of an iNKT TCR in complex with CD1d-lysophosphatidylcholine Deposited 2011-09-27 Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain C 21–295（275 aa）
Mutation：N42Q, N108Q, N163Q LSC (4R,7R,18E)-4,7-dihydroxy-N,N,N-trimethyl-10-oxo-3,5,9-trioxa-4-phosphaheptacos-18-en-1-aminium 4-oxide × 1 HEX HEXANE × 1 D12 DODECANE × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；0.1 M Hepes, 17% PEG 4000, 0.1 MgCl2, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 3.06 Å R-free 0.288
3U0P Crystal structure of human CD1d-lysophosphatidylcholine Deposited 2011-09-28 Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 21–295（275 aa）
Mutation：N42Q, N108Q, N163Q LSC (4R,7R,18E)-4,7-dihydroxy-N,N,N-trimethyl-10-oxo-3,5,9-trioxa-4-phosphaheptacos-18-en-1-aminium 4-oxide × 1 HEX HEXANE × 1 SO4 SULFATE ION × 3 GOL GLYCEROL × 4 UND UNDECANE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.1 M Tris-HCl, 2.0 M Ammonium Sulfate, 0.03 M glycyl-glycyl-glycine, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 2.80 Å R-free 0.259
3U0P Crystal structure of human CD1d-lysophosphatidylcholine Deposited 2011-09-28 Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain C 21–295（275 aa）
Mutation：N42Q, N108Q, N163Q LSC (4R,7R,18E)-4,7-dihydroxy-N,N,N-trimethyl-10-oxo-3,5,9-trioxa-4-phosphaheptacos-18-en-1-aminium 4-oxide × 1 SO4 SULFATE ION × 7 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.1 M Tris-HCl, 2.0 M Ammonium Sulfate, 0.03 M glycyl-glycyl-glycine, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 2.80 Å R-free 0.259
3U0P Crystal structure of human CD1d-lysophosphatidylcholine Deposited 2011-09-28 Assembly 3 Other combination Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain E 21–295（275 aa）
Mutation：N42Q, N108Q, N163Q SO4 SULFATE ION × 1 NBU N-BUTANE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.1 M Tris-HCl, 2.0 M Ammonium Sulfate, 0.03 M glycyl-glycyl-glycine, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 2.80 Å R-free 0.259
3VWJ Ternary crystal structure of the human NKT TCR-CD1d-C20:2 complex Deposited 2012-08-24 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain A 21–295（275 aa） Fragment：UNP residues 21-295
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 DB3 (11Z,14E)-N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]icosa-11,14-dienamide × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；295 K；8% PEG 10000, 0.2M magnesium chloride, 0.1M Tris, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 3.09 Å R-free 0.292
3VWK Ternary crystal structure of the human NKT TCR-CD1d-4'deoxy-alpha-galactosylceramide complex Deposited 2012-08-24 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain A 21–295（275 aa） Fragment：UNP residues 21-295
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 4GH N-{(2S,3R)-1-[(4-deoxy-alpha-D-xylo-hexopyranosyl)oxy]-3-hydroxyoctadecan-2-yl}hexacosanamide × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10；295 K；9% PEG 10000, 0.2M magnesium chloride, 0.1M glycine, pH 10.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.94 Å R-free 0.250
4EN3 Crystal structure of a human Valpha24(-) NKT TCR in complex with CD1d/alpha-galactosylceramide Deposited 2012-04-12 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain C 21–295（275 aa） Fragment：UNP residues 21-295
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 AGH N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE × 1 FUC alpha-L-fucopyranose × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；17 % PEG 4000, 0.1 M ammnonium acetate, 0.1 M sodium acetate pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 2.57 Å R-free 0.266
4LHU Crystal Structure of 9C2 TCR bound to CD1d Deposited 2013-07-01 Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain A 24–295（272 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 BMA beta-D-mannopyranose × 1 MG MAGNESIUM ION × 1 JLS (15Z)-N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]tetracos-15-enamide × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；12% PEG8000, 0.1 M Tris-HCl, pH 7.0, 0.2 M magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.87 Å R-free 0.243
4MNG Structure of the DP10.7 TCR with CD1d-sulfatide Deposited 2013-09-10 Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain A 21–201（181 aa） Fragment：CD1d,CD1d
Mutation：human CD1d alpha3 domain replaced with mouse CD1d alpha3 domain NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CIS (15Z)-N-((1S,2R,3E)-2-HYDROXY-1-{[(3-O-SULFO-BETA-D-GALACTOPYRANOSYL)OXY]METHYL}HEPTADEC-3-ENYL)TETRACOS-15-ENAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；11% PEG 4000 5% isopropanol 2 mM glutathione reduced/oxidized 50 mM tri-sodium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 3.01 Å R-free 0.207
4MNG Structure of the DP10.7 TCR with CD1d-sulfatide Deposited 2013-09-10 Assembly 2 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain C 21–201（181 aa） Fragment：CD1d,CD1d
Mutation：human CD1d alpha3 domain replaced with mouse CD1d alpha3 domain NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CIS (15Z)-N-((1S,2R,3E)-2-HYDROXY-1-{[(3-O-SULFO-BETA-D-GALACTOPYRANOSYL)OXY]METHYL}HEPTADEC-3-ENYL)TETRACOS-15-ENAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；11% PEG 4000 5% isopropanol 2 mM glutathione reduced/oxidized 50 mM tri-sodium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 3.01 Å R-free 0.207
4MQ7 Structure of human CD1d-sulfatide Deposited 2013-09-15 Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 21–202（182 aa） Fragment：human CD1d alpha1,2 domains fused with murine alpha3 domain
Mutation：residues from N-terminus through 184 are human sequence, residues from 185 to C-terminus are murine sequence NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CIS (15Z)-N-((1S,2R,3E)-2-HYDROXY-1-{[(3-O-SULFO-BETA-D-GALACTOPYRANOSYL)OXY]METHYL}HEPTADEC-3-ENYL)TETRACOS-15-ENAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；292 K；28% PEG 4000, 0.2 M CaCl2, 0.1 M Tris pH 9.0, vapor diffusion, sitting drop, temperature 292K
Resolution 2.60 Å R-free 0.284
4WO4 The molecular bases of Delta/Alpha beta T cell-mediated antigen recognition. Deposited 2014-10-15 Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain A 24–295（272 aa）
Not recorded JLS (15Z)-N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]tetracos-15-enamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；293 K；27% PEG1500 0.1M Sodium Malonate-imidazole-borate (2:3:3 molar ratio) 3% PEG3350
Resolution 2.50 Å R-free 0.237
4WW2 Crystal structure of human TCR Alpha Chain-TRAV21-TRAJ8, Beta Chain-TRBV7-8, Antigen-presenting glycoprotein CD1d, and Beta-2-microglobulin Deposited 2014-11-10 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain C 21–295（275 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 JLS (15Z)-N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]tetracos-15-enamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；9-10% PEG 6K 0.1M MES 6.0 4% Ethylene Glycol
Resolution 2.48 Å R-free 0.244
4WWK Crystal structure of human TCR Alpha Chain-TRAV12-3, Beta Chain-TRBV6-5, Antigen-presenting molecule CD1d, and Beta-2-microglobulin Deposited 2014-11-11 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain C 21–295（275 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 JLS (15Z)-N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]tetracos-15-enamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.5；293 K；18% PEG8000 0.1M CHES 9.5
Resolution 3.10 Å R-free 0.256
6V7Y Human CD1d presenting alpha-Galactosylceramide in complex with VHH nanobody 1D5 Deposited 2019-12-10 Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain A 23–296（274 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 SO4 SULFATE ION × 5 AGH N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE × 1 CL CHLORIDE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2M Ammonium Sulphate, 0.1M Tris-HCl pH 7.0, 0.2M Lithium Sulphate
Resolution 2.40 Å R-free 0.276
6V7Z Human CD1d presenting alpha-Galactosylceramide in complex with VHH nanobody 1D22 Deposited 2019-12-10 Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain A 23–296（274 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 AGH N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE × 1 PEG DI(HYDROXYETHYL)ETHER × 2 CL CHLORIDE ION × 1 SO4 SULFATE ION × 1 BGC beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；293 K；29% (v/v) PEG3350, 0.2M ammonium sulphate, 0.1M Bis-Tris (pH 5.3), 3% (v/v) glucose monohydrate
Resolution 2.75 Å R-free 0.252
6V7Z Human CD1d presenting alpha-Galactosylceramide in complex with VHH nanobody 1D22 Deposited 2019-12-10 Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain C 23–296（274 aa）
Not recorded AGH N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE × 1 PEG DI(HYDROXYETHYL)ETHER × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；293 K；29% (v/v) PEG3350, 0.2M ammonium sulphate, 0.1M Bis-Tris (pH 5.3), 3% (v/v) glucose monohydrate
Resolution 2.75 Å R-free 0.252
6V80 Crystal structure of human CD1d presenting alpha-Galactosylceramide in complex with NKT12 TCR and VHH nanobody 1D12 Deposited 2019-12-10 Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count
Chain A 23–296（274 aa）
Not recorded AGH N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；21 % (v/v) PEG 3350, 0.2 M tri-sodium citrate, 3% (v/v) D-(+)-trehalose dehydrate
Resolution 3.53 Å R-free 0.254
6V80 Crystal structure of human CD1d presenting alpha-Galactosylceramide in complex with NKT12 TCR and VHH nanobody 1D12 Deposited 2019-12-10 Assembly 2 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count
Chain F 23–296（274 aa）
Not recorded AGH N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；21 % (v/v) PEG 3350, 0.2 M tri-sodium citrate, 3% (v/v) D-(+)-trehalose dehydrate
Resolution 3.53 Å R-free 0.254
8SGB Crystal Structure of CD1d-lipid complexed with Beta-2-Microglobulin, TCR Alpha-Chain and TCR Beta-Chain Deposited 2023-04-12 Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain A 23–296（274 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 FO4 sphingomyelin × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, sodium citrate, citrate-bis-Tris pH7
Resolution 2.80 Å R-free 0.249
8SGM Crystal Structure of CD1d-lipid complexed with Beta-2-Microglobulin, TCR Alpha-Chain and TCR Beta-Chain Deposited 2023-04-12 Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain A 23–294（272 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 1 A1AHF N-[(2S)-3-oxo-1-(beta-L-talopyranosyloxy)octadecan-2-yl]docosanamide × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, sodium citrate, citrate-bis-Tris pH7
Resolution 2.50 Å R-free 0.234
8SOS Human CD1d presenting sphingomyelin C24:1 in complex with VHH nanobody 1D17 Deposited 2023-04-29 Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
Chain A 23–296（274 aa）
Chain E 23–296（274 aa）
Not recorded FO4 sphingomyelin × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；12% PEG8000, 0.05 M zinc acetate, 0.05 M MES, pH 6.2
Resolution 2.33 Å R-free 0.230
9O4X Gamma delta T cell receptor bound to CD1d Deposited 2025-04-09 Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain A 24–297（274 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 FO4 sphingomyelin × 1 1PE PENTAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；16% PEG 3350, 0.05M CBTP pH 5
Resolution 2.86 Å R-free 0.255

This page presents structural evidence recorded in PDB/mmCIF.“No recorded non-water small molecule” does not prove that the experimental sample was ligand-free; experimental conditions belong to the PDB experiment, while ligands and copy counts are shown for each biological assembly.