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3gml

Structure of mouse CD1d in complex with C6Ph

Method: X-RAY DIFFRACTION Dmax: 78.3 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

T-cell surface glycoprotein CD1d1

Mus musculus

UniProt P11609

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 19–297 Fragment：UNP residues 19-297 Beta-2 microglobulin × 1 （Q91XJ8） ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 C6Q N-{(1S,2S,3R)-1-[(alpha-D-galactopyranosyloxy)methyl]-2,3-dihydroxyheptadecyl}-6-phenylhexanamide × 1 PLM PALMITIC ACID × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.5；295 K；0.2 M Malonate pH 4.5, 20%(v/v) PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K Resolution 1.70 Å R-free 0.216

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3GML Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CD1 CD1(MOUSE) ANTIGEN PRESENTING MOLECULE Deposited 1997-04-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 22–336（315 aa） Fragment：ALPHA1, ALPHA2, ALPHA3, BETA2-MICROGLOBULIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；6 MG/ML PROTEIN 2.0M (NH4)2SO4 100 MM SODIUM CACODYLATE, 20MM EDTA, PH 6.5 5 UL PROTEIN + 2.5 UL RESERVOIR SITTING DROP, vapor diffusion - sitting drop
Resolution 2.67 Å R-free 0.330
1CD1 CD1(MOUSE) ANTIGEN PRESENTING MOLECULE Deposited 1997-04-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 22–336（315 aa） Fragment：ALPHA1, ALPHA2, ALPHA3, BETA2-MICROGLOBULIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；6 MG/ML PROTEIN 2.0M (NH4)2SO4 100 MM SODIUM CACODYLATE, 20MM EDTA, PH 6.5 5 UL PROTEIN + 2.5 UL RESERVOIR SITTING DROP, vapor diffusion - sitting drop
Resolution 2.67 Å R-free 0.330
2AKR Structural basis of sulfatide presentation by mouse CD1d Deposited 2005-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 19–297（279 aa） Fragment：extracellular domain, residues 19-297
Not recorded 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 pH 6.5；277 K；ammonium sulfate, NaCl, sodium cacodylate, manganese chloride, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K, pH 6.50
Resolution 1.90 Å R-free 0.249
2AKR Structural basis of sulfatide presentation by mouse CD1d Deposited 2005-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 19–297（279 aa） Fragment：extracellular domain, residues 19-297
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 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 pH 6.5；277 K；ammonium sulfate, NaCl, sodium cacodylate, manganese chloride, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K, pH 6.50
Resolution 1.90 Å R-free 0.249
2AKR Structural basis of sulfatide presentation by mouse CD1d Deposited 2005-08-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 19–297（279 aa） Fragment：extracellular domain, residues 19-297
Chain C 19–297（279 aa） Fragment：extracellular domain, residues 19-297
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 CIS (15Z)-N-((1S,2R,3E)-2-HYDROXY-1-{[(3-O-SULFO-BETA-D-GALACTOPYRANOSYL)OXY]METHYL}HEPTADEC-3-ENYL)TETRACOS-15-ENAMIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；277 K；ammonium sulfate, NaCl, sodium cacodylate, manganese chloride, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K, pH 6.50
Resolution 1.90 Å R-free 0.249
2AKR Structural basis of sulfatide presentation by mouse CD1d Deposited 2005-08-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 19–297（279 aa） Fragment：extracellular domain, residues 19-297
Chain C 19–297（279 aa） Fragment：extracellular domain, residues 19-297
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 CIS (15Z)-N-((1S,2R,3E)-2-HYDROXY-1-{[(3-O-SULFO-BETA-D-GALACTOPYRANOSYL)OXY]METHYL}HEPTADEC-3-ENYL)TETRACOS-15-ENAMIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；277 K；ammonium sulfate, NaCl, sodium cacodylate, manganese chloride, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K, pH 6.50
Resolution 1.90 Å R-free 0.249
2FIK Structure of a microbial glycosphingolipid bound to mouse CD1d Deposited 2005-12-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 19–297（279 aa） Fragment：extracellular domain of CD1d, residues 19-297
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GSL (2S,3R)-3-HYDROXY-2-(TETRADECANOYLAMINO)OCTADECYL ALPHA-D-GALACTOPYRANOSIDURONIC ACID × 1 PLM PALMITIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；20 % Polyethylene glycol 4000, 0.1 M sodium citrate, 10% isopropanol, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K
Resolution 1.80 Å R-free 0.243
2GAZ Mycobacterial lipoglycan presentation by CD1d Deposited 2006-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 19–297（279 aa） Fragment：extracellular domain, residues 19-297
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 XPX (2R)-3-[(HYDROXY{[(2R,3R,5S,6R)-3,4,5-TRIHYDROXY-2,6-BIS(ALPHA-D-MANNOPYRANOSYLOXY)CYCLOHEXYL]OXY}PHOSPHORYL)OXY]PROPAN E-1,2-DIYL DIHEXADECANOATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；20% Peg 4000, 0.1M sodium citrate, 10% n-propanol, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K
Resolution 2.61 Å R-free 0.280
2Q7Y Structure of the endogenous iNKT cell ligand iGb3 bound to mCD1d Deposited 2007-06-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 19–297（279 aa） Fragment：residues 19-297
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 IGC N-[(1S,2R,3E)-1-({[ALPHA-D-GALACTOPYRANOSYL-(1->3)-BETA-D-GALACTOPYRANOSYL-(1->4)-BETA-D-GLUCOPYRANOSYL]OXY}METHYL)-2-H YDROXYHEPTADEC-3-EN-1-YL]OCTANAMIDE × 1 PLM PALMITIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；295 K；18% PEG 4000, 0.2 M ammonium citrate, 2% butanol, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.95 Å R-free 0.245
2Q7Y Structure of the endogenous iNKT cell ligand iGb3 bound to mCD1d Deposited 2007-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 19–297（279 aa） Fragment：residues 19-297
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 IGC N-[(1S,2R,3E)-1-({[ALPHA-D-GALACTOPYRANOSYL-(1->3)-BETA-D-GALACTOPYRANOSYL-(1->4)-BETA-D-GLUCOPYRANOSYL]OXY}METHYL)-2-H YDROXYHEPTADEC-3-EN-1-YL]OCTANAMIDE × 1 PLM PALMITIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；295 K；18% PEG 4000, 0.2 M ammonium citrate, 2% butanol, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.95 Å R-free 0.245
3ARB Ternary crystal structure of the NKT TCR-CD1d-alpha-galactosylceramide analogue-OCH Deposited 2010-11-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 19–297（279 aa） Fragment：heavy chain
Not recorded PEG DI(HYDROXYETHYL)ETHER × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 FEE N-{(1S,2S,3R)-1-[(alpha-D-galactopyranosyloxy)methyl]-2,3-dihydroxyoctyl}tetracosanamide × 1 D12 DODECANE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；22% PEG 400, 0.1M Ammonium acetate, 0.1M Bis Tris, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.70 Å R-free 0.257
3ARD Ternary crystal structure of the mouse NKT TCR-CD1d-3'deoxy-alpha-galactosylceramide Deposited 2010-11-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 19–297（279 aa） Fragment：heavy chain
Not recorded 3GH N-{(2S,3R)-1-[(3-deoxy-alpha-D-xylo-hexopyranosyl)oxy]-3-hydroxyoctadecan-2-yl}hexacosanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；20% PEG 400, 0.1 Ammonium acetate, 0.1M Bis Tris, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 3.01 Å R-free 0.277
3ARE Ternary crystal structure of the mouse NKT TCR-CD1d-4'deoxy-alpha-galactosylceramide Deposited 2010-11-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 19–297（279 aa） Fragment：heavy chain
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 4GH N-{(2S,3R)-1-[(4-deoxy-alpha-D-xylo-hexopyranosyl)oxy]-3-hydroxyoctadecan-2-yl}hexacosanamide × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；20% PEG 400, 0.1M Ammonium acetate, 0.1M Bis Tris, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.80 Å R-free 0.279
3ARF Ternary crystal structure of the mouse NKT TCR-CD1d-C20:2 Deposited 2010-11-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 19–297（279 aa） Fragment：heavy chain
Not recorded DB3 (11Z,14E)-N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]icosa-11,14-dienamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；20% PEG 400, 0.1M Ammonium acetate, 0.1M Bis Tris, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.90 Å R-free 0.277
3ARG Ternary crystal structure of the mouse NKT TCR-CD1d-alpha-glucosylceramide(C20:2) Deposited 2010-11-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 19–297（279 aa） Fragment：heavy chain
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 DB6 (11E,14E)-N-[(2S,3S,4R)-1-(alpha-D-glucopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]icosa-11,14-dienamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；20% PEG 400, 0.1M Ammonium acetate, 0.1M Bis Tris, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 3.00 Å R-free 0.300
3AU1 Crystal structure of mouse CD1d in complex with ganglioside GD3 Deposited 2011-01-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 19–297（279 aa） Fragment：extracellular domain
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ERA (7Z,15E,17E)-N-[(2S,3S,4E)-1,3-dihydroxyoctadec-4-en-2-yl]tricosa-7,15,17-trienamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；22% PEG 4000, 10% isopropanol, 0.1M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.50 Å R-free 0.238
3G08 Crystal structure of the alpha-galactosylceramide analog OCH in complex with mouse CD1d Deposited 2009-01-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 19–297（279 aa） Fragment：UNP residues 19-298
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 FEE N-{(1S,2S,3R)-1-[(alpha-D-galactopyranosyloxy)methyl]-2,3-dihydroxyoctyl}tetracosanamide × 1 PLM PALMITIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；16% polyethylene glycol 3350, 100mM Tris pH8.5, 2% tacsimate pH8.0 , VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.60 Å R-free 0.226
3GMM Structure of mouse CD1d in complex with C8Ph Deposited 2009-03-14 Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 19–297（279 aa） Fragment：UNP residues 19-297
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 C8P N-{(1S,2S,3R)-1-[(alpha-D-galactopyranosyloxy)methyl]-2,3-dihydroxyheptadecyl}-8-phenyloctanamide × 1 PLM PALMITIC ACID × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；295 K；0.2 M Malonate pH 4.5, 20%(v/v) PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.80 Å R-free 0.219
3GMN Structure of mouse CD1d in complex with C10Ph Deposited 2009-03-14 Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 19–297（279 aa） Fragment：UNP residues 19-297
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 C1Q N-{(1S,2S,3R)-1-[(alpha-D-galactopyranosyloxy)methyl]-2,3-dihydroxyheptadecyl}-10-phenyldecanamide × 1 PLM PALMITIC ACID × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；295 K；0.2 M Malonate pH 4.5, 20%(v/v) PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.70 Å R-free 0.218
3GMO Structure of mouse CD1d in complex with C8PhF Deposited 2009-03-14 Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 19–297（279 aa） Fragment：UNP residues 19-297
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 C8F 8-(4-fluorophenyl)-N-{(1S,2S,3R)-1-[(alpha-D-galactopyranosyloxy)methyl]-2,3-dihydroxyheptadecyl}octanamide × 1 PLM PALMITIC ACID × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；295 K；0.2 M Malonate pH 4.5, 20%(v/v) PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.60 Å R-free 0.216
3GMP Structure of mouse CD1d in complex with PBS-25 Deposited 2009-03-14 Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 19–297（279 aa） Fragment：UNP residues 19-297
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PBS (2S,3S,4R)-N-OCTANOYL-1-[(ALPHA-D-GALACTOPYRANOSYL)OXY]-2-AMINO-OCTADECANE-3,4-DIOL × 1 PLM PALMITIC ACID × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；295 K；0.2 M Malonate pH 4.5, 20%(v/v) PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.70 Å R-free 0.216
3GMQ Structure of mouse CD1d expressed in SF9 cells, no ligand added Deposited 2009-03-14 Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 19–297（279 aa） Fragment：UNP residues 19-297
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PLM PALMITIC ACID × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；295 K；0.2 M Malonate pH 4.5, 20%(v/v) PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.80 Å R-free 0.231
3GMR Structure of mouse CD1d in complex with C8Ph, different space group Deposited 2009-03-14 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 19–297（279 aa） Fragment：UNP residues 19-297
Not recorded C8P N-{(1S,2S,3R)-1-[(alpha-D-galactopyranosyloxy)methyl]-2,3-dihydroxyheptadecyl}-8-phenyloctanamide × 1 PLM PALMITIC ACID × 1 EDO 1,2-ETHANEDIOL × 4 PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；295 K；0.2 M Malonate pH 4.5, 20%(v/v) PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.90 Å R-free 0.230
3HE6 Crystal structure of mouse CD1d-alpha-galactosylceramide with mouse Valpha14-Vbeta8.2 NKT TCR Deposited 2009-05-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 19–297（279 aa） Fragment：extracellular domain
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 5.5；298 K；17% polyethylene glycol 10K, 0.1M ammonium acetate, 0.1M BisTris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.90 Å R-free 0.298
3HE7 Crystal structure of mouse CD1d-alpha-galactosylceramide with mouse Valpha14-Vbeta7 NKT TCR Deposited 2009-05-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 19–297（279 aa） Fragment：extracellular domain
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 5.5；298 K；17% polyethylene glycol 10K, 0.1M ammonium acetate, 0.1M Bis Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.80 Å R-free 0.271
3ILP Structure of mCD1d with bound glycolipid BbGL-2f from Borrelia burgdorferi Deposited 2009-08-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 19–297（279 aa） Fragment：UNP residues 19-298
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 1L2 (2S)-3-(alpha-D-galactopyranosyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl (9Z,12Z)-octadeca-9,12-dienoate × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；295 K；20% polyethylene glycol 4000, 100mM sodium citrate, 10% n-propanol, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.85 Å R-free 0.233
3ILQ Structure of mCD1d with bound glycolipid BbGL-2c from Borrelia burgdorferi Deposited 2009-08-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 19–297（279 aa） Fragment：UNP residues 19-298
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 1O2 (2S)-3-(alpha-D-galactopyranosyloxy)-2-(hexadecanoyloxy)propyl (9Z)-octadec-9-enoate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；295 K；17% polyethylene glycol 3350, 150mM di-ammonium hydrogen citrate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 2.05 Å R-free 0.251
3MA7 Crystal structure of Cardiolipin bound to mouse CD1D Deposited 2010-03-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 19–297（279 aa） Fragment：UNP RESIDUES 19-297
Not recorded CD4 (2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate × 1 PLM PALMITIC ACID × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 20% POLYETHYLENE GLYCOL 4000, 300MM CALCIUM ACETATE, 6% ETHYLENE GLYCOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K
Resolution 2.29 Å R-free 0.273
3MA7 Crystal structure of Cardiolipin bound to mouse CD1D Deposited 2010-03-23 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 19–297（279 aa） Fragment：UNP RESIDUES 19-297
Not recorded CD4 (2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate × 1 PLM PALMITIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 20% POLYETHYLENE GLYCOL 4000, 300MM CALCIUM ACETATE, 6% ETHYLENE GLYCOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K
Resolution 2.29 Å R-free 0.273
3O8X Recognition of Glycolipid Antigen by iNKT Cell TCR Deposited 2010-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 19–297（279 aa） Fragment：residues 19-297
Not recorded GSL (2S,3R)-3-HYDROXY-2-(TETRADECANOYLAMINO)OCTADECYL ALPHA-D-GALACTOPYRANOSIDURONIC ACID × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；295 K；18% polyethylene glycol 3350, 0.2 M ammonium citrate dibasic, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 2.74 Å R-free 0.253
3O9W Recognition of a Glycolipid Antigen by the iNKT Cell TCR Deposited 2010-08-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 19–297（279 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 1O2 (2S)-3-(alpha-D-galactopyranosyloxy)-2-(hexadecanoyloxy)propyl (9Z)-octadec-9-enoate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；295 K；20% polyethylene glycol 3350, 0.1 M citrate pH 5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 2.80 Å R-free 0.258
3QI9 Crystal structure of mouse CD1d-alpha-phosphotidylinositol with mouse Valpha14-Vbeta6 2A3-D NKT TCR Deposited 2011-01-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 19–297（279 aa） Fragment：residues in UNP 19-297
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 PII 2-[(HYDROXY{[(2R,3R,5S,6R)-2,3,4,5,6-PENTAHYDROXYCYCLOHEXYL]OXY}PHOSPHORYL)OXY]-1-[(PALMITOYLOXY)METHYL]ETHYL HEPTADECANOATE × 1 MG MAGNESIUM ION × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；296 K；PEG 6000, Sodium Citrate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 2.30 Å R-free 0.275
3QUX Structure of the mouse CD1d-alpha-C-GalCer-iNKT TCR complex Deposited 2011-02-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 19–297（279 aa） Fragment：UNP residues 19-297
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 QUX N-[(3S,4S,5R)-4,5-dihydroxy-1-[(2R,3R,4R,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]nonadecan-3-yl]hexacosanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；20% polyethylene glycol 3350, 8% tacsimate, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 2.91 Å R-free 0.252
3QUY Structure of the mouse CD1d-BnNH-GSL-1'-iNKT TCR complex Deposited 2011-02-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 19–297（279 aa） Fragment：UNP residues 19-297
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 QUY (2S,3R,4S,5R,6S)-6-[(2S,3S,4R)-2-(hexacosanoylamino)-3,4-dihydroxy-octadecoxy]-3,4,5-trihydroxy-N-(phenylmethyl)oxane-2-carboxamide × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；295 K；17% polyethylene glycol 4000, 0.1 M citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 2.25 Å R-free 0.231
3QUZ Structure of the mouse CD1d-NU-alpha-GalCer-iNKT TCR complex Deposited 2011-02-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 19–297（279 aa） Fragment：UNP residues 19-297
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 QUV N-[(2S,3S,4R)-1-({6-deoxy-6-[(naphthalen-1-ylcarbamoyl)amino]-alpha-D-galactopyranosyl}oxy)-3,4-dihydroxyoctadecan-2-yl]hexacosanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；20% polyethylene glycole, 0.2 M ammonium citrate dibasic, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 2.30 Å R-free 0.233
3RTQ Structure of the mouse CD1d-HS44-iNKT TCR complex Deposited 2011-05-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 19–297（279 aa） Fragment：UNP residues 19-297
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 H4S N-[(2S,3S,4R)-3,4-dihydroxy-1-{[(1S,2S,3R,4R,5S)-2,3,4,5-tetrahydroxycyclohexyl]amino}octadecan-2-yl]hexacosanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；295 K；16% polyethylene glycol 3350, 8% v/v Tacsimate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 2.80 Å R-free 0.268
3RUG Crystal structure of Valpha10-Vbeta8.1 NKT TCR in complex with CD1d-alphaglucosylceramide (C20:2) Deposited 2011-05-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 19–297（279 aa） Fragment：extracellular domain
Not recorded DB6 (11E,14E)-N-[(2S,3S,4R)-1-(alpha-D-glucopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]icosa-11,14-dienamide × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；20% PEG 1500, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.20 Å R-free 0.254
3RUG Crystal structure of Valpha10-Vbeta8.1 NKT TCR in complex with CD1d-alphaglucosylceramide (C20:2) Deposited 2011-05-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 19–297（279 aa） Fragment：extracellular domain
Not recorded DB6 (11E,14E)-N-[(2S,3S,4R)-1-(alpha-D-glucopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]icosa-11,14-dienamide × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；20% PEG 1500, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.20 Å R-free 0.254
3RZC Structure of the self-antigen iGb3 bound to mouse CD1d and in complex with the iNKT TCR Deposited 2011-05-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 19–297（279 aa） Fragment：19-298
Not recorded LGN N-[(2S,3R,4E)-1-{[alpha-D-galactopyranosyl-(1->3)-beta-D-galactopyranosyl-(1->4)-beta-D-glucopyranosyl]oxy}-3-hydroxyoctadec-4-en-2-yl]hexacosanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；300 K；16% polyethylene glycol 3350, 8% tacsimate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 300K
Resolution 2.80 Å R-free 0.271
3SCM Crystal structure of autoreactive-Valpha14-Vbeta6 NKT TCR in complex with CD1d-isoglobotrihexosylceramide Deposited 2011-06-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 19–297（279 aa） Fragment：extracellular domain, UNP residues 19-297
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 LGN N-[(2S,3R,4E)-1-{[alpha-D-galactopyranosyl-(1->3)-beta-D-galactopyranosyl-(1->4)-beta-D-glucopyranosyl]oxy}-3-hydroxyoctadec-4-en-2-yl]hexacosanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；0.1M Sodium citrate, 14% PEG 6000, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.318
3SDA Crystal structure of autoreactive-Valpha14-Vbeta6 NKT TCR in complex with CD1d-beta-galactosylceramide Deposited 2011-06-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 19–297（279 aa） Fragment：extracellular domain, UNP residues 19-297
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GCY N-[(2S,3R)-1-(beta-D-galactopyranosyloxy)-3-hydroxyoctadec-4-en-2-yl]tetracosanamide × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；0.1M Sodium Citrate, 15% PEG 6000, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å R-free 0.312
3SDC Crystal structure of autoreactive-Valpha14-Vbeta6 NKT TCR in complex with CD1d-globotrihexosylceramide Deposited 2011-06-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 19–297（279 aa） Fragment：extracellular domain, UNP residues 19-297
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 3GB N-[(2S,3R,4E)-1-{[alpha-D-galactopyranosyl-(1->4)-beta-D-galactopyranosyl-(1->4)-beta-D-glucopyranosyl]oxy}-3-hydroxyoctadec-4-en-2-yl]hexacosanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；13.5% PEG 6000, 0.1M Sodium citrate, pH 6.1, vapor diffusion, hanging drop, temperature 293K
Resolution 3.10 Å R-free 0.292
3SDD Crystal structure of autoreactive-Valpha14-Vbeta6 NKT TCR in complex with CD1d-beta-lactosylceramide Deposited 2011-06-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 19–297（279 aa） Fragment：extracellular domain, UNP residues 19-297
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 3GD N-[(2S,3R,4E)-1-{[4-O-(beta-D-galactopyranosyl)-beta-D-glucopyranosyl]oxy}-3-hydroxyoctadec-4-en-2-yl]docosanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；16% PEG 6000, 0.1M Sodium citrate, pH 6.0, vapor diffusion, hanging drop, temperature 293K
Resolution 3.00 Å R-free 0.318
3T1F Crystal structure of the mouse CD1d-Glc-DAG-s2 complex Deposited 2011-07-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 19–297（279 aa） Fragment：UNP residues 19-298
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 3TF (2S)-1-(alpha-D-glucopyranosyloxy)-3-(hexadecanoyloxy)propan-2-yl (11Z)-octadec-11-enoate × 1 GOL GLYCEROL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；8% tacsimate pH 7.5, 17% PEG3350 , VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.70 Å R-free 0.219
3TA3 Structure of the mouse CD1d-Glc-DAG-s2-iNKT TCR complex Deposited 2011-08-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 19–297（279 aa） Fragment：Residues 19-297
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 3TF (2S)-1-(alpha-D-glucopyranosyloxy)-3-(hexadecanoyloxy)propan-2-yl (11Z)-octadec-11-enoate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；295 K；17% PEG 3350, 8% tacsimate pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 2.70 Å R-free 0.256
3TN0 Structure of mouse Va14Vb8.2NKT TCR-mouse CD1d-a-C-Galactosylceramide complex Deposited 2011-09-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 19–297（279 aa） Fragment：UNP residues 19-297
Not recorded QUX N-[(3S,4S,5R)-4,5-dihydroxy-1-[(2R,3R,4R,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]nonadecan-3-yl]hexacosanamide × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；15-17% PEG 10K, 0.1M ammonium acetat, 0.1M BisTris pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 3.20 Å R-free 0.289
3TO4 Structure of mouse Valpha14Vbeta2-mouseCD1d-alpha-Galactosylceramide Deposited 2011-09-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 19–297（279 aa） Fragment：UNP residues 19-297
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；pH 5.5；295 K；17% PEG 10K, 0.1M ammonium acetate, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 3.10 Å R-free 0.268
3TVM Structure of the mouse CD1d-SMC124-iNKT TCR complex Deposited 2011-09-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 19–297（279 aa） Fragment：residues 19-298
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 07P N-[(2S,3R)-10-[(1R,2R)-2-decylcyclopropyl]-1-(alpha-D-galactopyranosyloxy)-3-hydroxydecan-2-yl]hexacosanamide × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；295 K；100mM trisodium citrate pH5.6, 10% PEG3350, 2% tacsimate pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 2.80 Å R-free 0.273
3TVM Structure of the mouse CD1d-SMC124-iNKT TCR complex Deposited 2011-09-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 19–297（279 aa） Fragment：residues 19-298
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 07P N-[(2S,3R)-10-[(1R,2R)-2-decylcyclopropyl]-1-(alpha-D-galactopyranosyloxy)-3-hydroxydecan-2-yl]hexacosanamide × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；295 K；100mM trisodium citrate pH5.6, 10% PEG3350, 2% tacsimate pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 2.80 Å R-free 0.273
3UBX Crystal structure of the mouse CD1d-C20:2-aGalCer-L363 mAb Fab complex Deposited 2011-10-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 19–297（279 aa） Fragment：UNP residues 19-297
Not recorded 09N (11Z,14Z)-N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]icosa-11,14-dienamide × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；12% PEG3350, 4% v/v Tacsimate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 3.10 Å R-free 0.230
3UBX Crystal structure of the mouse CD1d-C20:2-aGalCer-L363 mAb Fab complex Deposited 2011-10-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 19–297（279 aa） Fragment：UNP residues 19-297
Not recorded 09N (11Z,14Z)-N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]icosa-11,14-dienamide × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；12% PEG3350, 4% v/v Tacsimate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 3.10 Å R-free 0.230
4APQ Crystal structure of autoreactive-Valpha14-Vbeta6 NKT TCR in complex with CD1d-sulfatide Deposited 2012-04-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 19–297（279 aa） Fragment：EXTRACELLULAR DOMAIN, RESIDUES 19-297
Not recorded 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 pH 6.2；0.2M SODIUM CITRATE PH 6.2, 15% PEG 6000
Resolution 3.00 Å R-free 0.232
4EI5 Crystal Structure of XV19 TCR in complex with CD1d-sulfatide C24:1 Deposited 2012-04-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 19–297（279 aa） Fragment：UNP residues 19-297
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 FLC CITRATE ANION × 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, HANGING DROP；pH 7.1；277 K；25% PEG3350, 0.1 M citrate/Bis-Tris-propane, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.10 Å R-free 0.227
4EI5 Crystal Structure of XV19 TCR in complex with CD1d-sulfatide C24:1 Deposited 2012-04-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 19–297（279 aa） Fragment：UNP residues 19-297
Not recorded 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, HANGING DROP；pH 7.1；277 K；25% PEG3350, 0.1 M citrate/Bis-Tris-propane, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.10 Å R-free 0.227
4ELM Crystal structure of the mouse CD1d-lysosulfatide-Hy19.3 TCR complex Deposited 2012-04-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 19–297（279 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 SGF (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl 3-O-sulfo-beta-D-galactopyranoside × 1 PLM PALMITIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；11% PEG4000, 4% tacsimate, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 3.48 Å R-free 0.265
4ELM Crystal structure of the mouse CD1d-lysosulfatide-Hy19.3 TCR complex Deposited 2012-04-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 19–297（279 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 SGF (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl 3-O-sulfo-beta-D-galactopyranoside × 1 PLM PALMITIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；11% PEG4000, 4% tacsimate, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 3.48 Å R-free 0.265
4IRJ Structure of the mouse CD1d-4ClPhC-alpha-GalCer-iNKT TCR complex Deposited 2013-01-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 19–297（279 aa） Fragment：UNP residues 19-298
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 1L9 N-[(2S,3S,4R)-1-({6-O-[(4-chlorophenyl)carbamoyl]-alpha-D-galactopyranosyl}oxy)-3,4-dihydroxyoctadecan-2-yl]hexacosanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295.5 K；20% polyethylene glycol 4000, 0.2M sodium thiocyanate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.5K
Resolution 3.00 Å R-free 0.228
4IRS Structure of the mouse CD1d-PyrC-alpha-GalCer-iNKT TCR complex Deposited 2013-01-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 19–297（279 aa） Fragment：UNP residues 19-298
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 1LA N-[(2S,3S,4R)-3,4-dihydroxy-1-{[6-O-(pyridin-4-ylcarbamoyl)-alpha-D-galactopyranosyl]oxy}octadecan-2-yl]hexacosanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295.5 K；20% polyethylene glycol 4000, 0.2M di-ammonium hydrogen citrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.5K
Resolution 2.80 Å R-free 0.239
4MX7 Structure of mouse CD1d in complex with dioleoyl-phosphatidic acid Deposited 2013-09-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 19–297（279 aa） Fragment：CD1d ectdomain, UNP residues 19-297
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 MX7 (2R)-3-(phosphonooxy)propane-1,2-diyl (9Z,9'Z)bis-octadec-9-enoate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；20% PEG 4000, 0.2M ammonium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.24 Å R-free 0.252
4Y16 Crystal structure of the mCD1d/NC-aGC/iNKTCR ternary complex Deposited 2015-02-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 19–297（279 aa） Fragment：Ectodomain, UNP residues 19-297
Not recorded 48G N-[(2S,3S,4R)-3,4-dihydroxy-1-{[6-O-(naphthalen-1-ylcarbamoyl)-alpha-D-galactopyranosyl]oxy}octadecan-2-yl]hexacosanamide × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295.5 K；20% PEG 4000, 0.2M Di-ammonium hydrogen citrate
Resolution 2.60 Å R-free 0.244
4Y2D Crystal structure of the mCD1d/7DW8-5/iNKTCR ternary complex Deposited 2015-02-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 19–297（279 aa） Fragment：Ectodomain, UNP residues 19-297
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 7DW 11-(4-fluorophenyl)-N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]undecanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295.5 K；17% PEG 4000, 8% tascimate pH 4.0
Resolution 3.05 Å R-free 0.257
4Y2D Crystal structure of the mCD1d/7DW8-5/iNKTCR ternary complex Deposited 2015-02-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 19–297（279 aa） Fragment：Ectodomain, UNP residues 19-297
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 7DW 11-(4-fluorophenyl)-N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]undecanamide × 1 FUC alpha-L-fucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295.5 K；17% PEG 4000, 8% tascimate pH 4.0
Resolution 3.05 Å R-free 0.257
4Y4F Crystal structure of the mCD1d/GCK127/iNKTCR ternary complex Deposited 2015-02-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 19–297（279 aa） Fragment：Ectodomain, UNP residues 19-297
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 49M (1R)-1,5-anhydro-1-[(1E,3S,4S,5R)-4,5-dihydroxy-3-(nonacosanoylamino)nonadec-1-en-1-yl]-D-galactitol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295.5 K；17% PEG 4000, 0.2M potassium acetate
Resolution 3.19 Å R-free 0.257
4Y4F Crystal structure of the mCD1d/GCK127/iNKTCR ternary complex Deposited 2015-02-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 19–297（279 aa） Fragment：Ectodomain, UNP residues 19-297
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 49M (1R)-1,5-anhydro-1-[(1E,3S,4S,5R)-4,5-dihydroxy-3-(nonacosanoylamino)nonadec-1-en-1-yl]-D-galactitol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295.5 K；17% PEG 4000, 0.2M potassium acetate
Resolution 3.19 Å R-free 0.257
4Y4H Crystal structure of the mCD1d/GCK152/iNKTCR ternary complex Deposited 2015-02-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 19–297（279 aa） Fragment：Ectodomain, UNP residues 19-297
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 49X (1R)-1,5-anhydro-1-{(1E,3S,4S,5R)-4,5-dihydroxy-3-[(8-phenyloctanoyl)amino]nonadec-1-en-1-yl}-D-galactitol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295.5 K；16% PEG 4000, 0.2M di-ammonium hydrogen citrate
Resolution 3.10 Å R-free 0.287
4Y4H Crystal structure of the mCD1d/GCK152/iNKTCR ternary complex Deposited 2015-02-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 19–297（279 aa） Fragment：Ectodomain, UNP residues 19-297
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 49X (1R)-1,5-anhydro-1-{(1E,3S,4S,5R)-4,5-dihydroxy-3-[(8-phenyloctanoyl)amino]nonadec-1-en-1-yl}-D-galactitol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295.5 K；16% PEG 4000, 0.2M di-ammonium hydrogen citrate
Resolution 3.10 Å R-free 0.287
4Y4K Crystal structure of the mCD1d/EF77/iNKTCR ternary complex Deposited 2015-02-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 19–297（279 aa） Fragment：Ectodomain, UNP residues 19-297
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 49Y (4Z)-9-[(1R,2R)-2-decylcyclopropyl]-N-[(2S,3S,4S)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]non-4-enamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295.5 K；20% PEG 4000, 0.2M ammonium citrate dibasic
Resolution 2.90 Å R-free 0.267
4ZAK Crystal structure of the mCD1d/DB06-1/iNKTCR ternary complex Deposited 2015-04-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 19–297（279 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 4LX N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]hexacosanethioamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；295 K；20% PEG 4000, 0.2M ammonium citrate dibasic
Resolution 2.82 Å R-free 0.256
5EFI Crystal structure of mouse CD1d in complex with the p99p lipopeptide Deposited 2015-10-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 19–297（279 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CIT CITRIC ACID × 1 NA SODIUM ION × 1 PLM PALMITIC ACID × 1 OCA OCTANOIC ACID (CAPRYLIC ACID) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；ammonium citrate, PEG4000
Resolution 1.80 Å R-free 0.244
5FKP Crystal structure of the mouse CD1d in complex with the p99 peptide Deposited 2015-10-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 19–297（279 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 6UL TETRACOSYL PALMITATE × 1 GOL GLYCEROL × 4 TAR D(-)-TARTARIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 0.2M AMMONIUM TARTRATE AND 20% PEG4000
Resolution 1.80 Å R-free 0.234
5TW2 Structure of mouse CD1d with bound alpha-galactosylsphingamide JG168 Deposited 2016-11-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 19–297（279 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 7LP (5R,6S,7S)-5,6-dihydroxy-7-(octanoylamino)-N-(6-phenylhexyl)-8-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]oxy}octanamide × 1 PLM PALMITIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；295 K；20% PEG 4000, 8% Tacsimate
Resolution 1.75 Å R-free 0.221
5TW5 Structure of mouse CD1d with bound glycosphingolipid JJ112 Deposited 2016-11-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 19–297（279 aa）
Not recorded PLM PALMITIC ACID × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 7LM N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxy-16-phenylhexadecan-2-yl]octanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；20% PEG 3350, 200 mM sodium malonate
Resolution 1.85 Å R-free 0.244
5VCJ Structure of alpha-galactosylphytosphingosine bound by CD1d and in complex with the Va14Vb8.2 TCR Deposited 2017-03-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 19–297（279 aa） Fragment：Ectodomain (UNP residues 19-297)
Mutation：D201H N57 (2S,3S,4R)-2-amino-3,4-dihydroxyoctadecyl alpha-D-galactopyranoside × 1 PLM PALMITIC ACID × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；295 K；20 % polyethylene glycol 3350, 200 mM sodium malonate
Resolution 3.16 Å R-free 0.248
6CW6 Structure of alpha-GC[8,18] bound by CD1d and in complex with the Va14Vb8.2 TCR Deposited 2018-03-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 19–297（279 aa） Fragment：residues 19-297
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 PBS (2S,3S,4R)-N-OCTANOYL-1-[(ALPHA-D-GALACTOPYRANOSYL)OXY]-2-AMINO-OCTADECANE-3,4-DIOL × 1 PLM PALMITIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；295 K；8% Tacsimate pH 4.0 20% PEG 3350
Resolution 2.85 Å R-free 0.250
6MSS Diversity in the type II Natural Killer T cell receptor repertoire and antigen specificity leads to differing CD1d docking strategies Deposited 2018-10-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 19–297（279 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 SRV (2S)-2-(heptadecanoyloxy)-3-{[(10S)-10-methyloctadecanoyl]oxy}propyl alpha-D-glucopyranosiduronic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；15-25% PEG 1500 10% succinate phosphate glycine pH 6.8
Resolution 3.00 Å R-free 0.242
6XNG MHC-like protein complex structure Deposited 2020-07-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 19–297（279 aa）
Not recorded V8P (3R)-N-[(2S,3R)-1-(alpha-D-galactopyranosyloxy)-3-hydroxyheptadecan-2-yl]-3-hydroxyheptadecanamide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；18-20% PEG 3350, 8% Tacsimate pH 5.0
Resolution 2.79 Å R-free 0.277
7M72 MHC-like protein complex structure Deposited 2021-03-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 19–297（279 aa）
Not recorded QOD (3R)-N-[(2S,3R)-1-(alpha-D-galactopyranosyloxy)-3-hydroxy-15-methylhexadecan-2-yl]-3-hydroxyheptadecanamide × 1 HP6 HEPTANE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；18-20% PEG 3350, 8% Tacsimate pH 5.0
Resolution 2.40 Å R-free 0.227
8T4Z T-cell receptor and lipid complex structure Deposited 2023-06-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 19–297（279 aa）
Not recorded Y73 N-[(2R,3R,4E)-1,3-dihydroxyoctadec-4-en-2-yl]tetracosanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；18-20% PEG3350, 8% Tacsimate pH 5.0
Resolution 2.69 Å R-free 0.265

64 other PDB entries and 78 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CD1D1_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–279； UniProt 19–297

Beta-2 microglobulin

Mus musculus

UniProt Q91XJ8

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 21–119 Fragment：UNP residues 21-119 T-cell surface glycoprotein CD1d1 × 1 （P11609） ;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 C6Q N-{(1S,2S,3R)-1-[(alpha-D-galactopyranosyloxy)methyl]-2,3-dihydroxyheptadecyl}-6-phenylhexanamide × 1 PLM PALMITIC ACID × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.5；295 K；0.2 M Malonate pH 4.5, 20%(v/v) PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K Resolution 1.70 Å R-free 0.216

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3GML Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2QRI Crystal structure of a single chain trimer composed of the MHC I heavy chain H-2Kb WT, beta-2microglobulin, and ovalbumin-derived peptide. Deposited 2007-07-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 21–119（99 aa） Fragment：;Fusion protein of ovalbumin-derived peptide, linker, Beta-2 microglobulin, linker, and H-2 class I histocompatibility antigen K-B alpha chain extracellular domain ;
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；298 K；13% PEG 10000, 100 mM MES, pH 6.2, vapor diffusion, hanging drop, temperature 298K
Resolution 2.00 Å R-free 0.253
2QRI Crystal structure of a single chain trimer composed of the MHC I heavy chain H-2Kb WT, beta-2microglobulin, and ovalbumin-derived peptide. Deposited 2007-07-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 21–119（99 aa） Fragment：;Fusion protein of ovalbumin-derived peptide, linker, Beta-2 microglobulin, linker, and H-2 class I histocompatibility antigen K-B alpha chain extracellular domain ;
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；298 K；13% PEG 10000, 100 mM MES, pH 6.2, vapor diffusion, hanging drop, temperature 298K
Resolution 2.00 Å R-free 0.253
2QRS Crystal Structure of a single chain trimer composed of the MHC I heavy chain H-2Kb Y84A, beta-2microglobulin, and ovalbumin-derived peptide. Deposited 2007-07-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 21–119（99 aa） Fragment：;Fusion protein of ovalbumin-derived peptide, linker, Beta-2 microglobulin, linker, and H-2 class I histocompatibility antigen K-B alpha chain extracellular domain ;
Mutation：Y105A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；298 K；14% PEG 6000, 100 mM MES, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.252
2QRS Crystal Structure of a single chain trimer composed of the MHC I heavy chain H-2Kb Y84A, beta-2microglobulin, and ovalbumin-derived peptide. Deposited 2007-07-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 21–119（99 aa） Fragment：;Fusion protein of ovalbumin-derived peptide, linker, Beta-2 microglobulin, linker, and H-2 class I histocompatibility antigen K-B alpha chain extracellular domain ;
Mutation：Y105A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；298 K；14% PEG 6000, 100 mM MES, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.252
2QRT Crystal Structure of a disulfide trapped single chain trimer composed of the MHC I heavy chain H-2Kb Y84C, beta-2microglobulin, and ovalbumin-derived peptide. Deposited 2007-07-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 21–119（99 aa） Fragment：;Fusion protein of ovalbumin-derived peptide, linker, Beta-2 microglobulin, linker, and H-2 class I histocompatibility antigen K-B alpha chain extracellular domain ;
Mutation：Y105C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；298 K；13% PEG 6000, 100 mM MES, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.80 Å R-free 0.239
2QRT Crystal Structure of a disulfide trapped single chain trimer composed of the MHC I heavy chain H-2Kb Y84C, beta-2microglobulin, and ovalbumin-derived peptide. Deposited 2007-07-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 21–119（99 aa） Fragment：;Fusion protein of ovalbumin-derived peptide, linker, Beta-2 microglobulin, linker, and H-2 class I histocompatibility antigen K-B alpha chain extracellular domain ;
Mutation：Y105C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；298 K；13% PEG 6000, 100 mM MES, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.80 Å R-free 0.239
3C8K The crystal structure of Ly49C bound to H-2Kb Deposited 2008-02-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 21–119（99 aa） Fragment：UNP residues 21-119
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；277 K；2.0 M ammonium sulfate, 2% (volume/volume) PEG 400 and 0.1 M Hepes, pH 7.5, VAPOR DIFFUSION, temperature 277K
Resolution 2.90 Å R-free 0.263
3DMM Crystal structure of the CD8 alpha beta/H-2Dd complex Deposited 2008-07-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 21–119（99 aa） Fragment：Residues 21-119
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；291 K；12% PEG 3000, 0.05M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.60 Å R-free 0.292
3E6F MHC CLASS I H-2Dd Heavy chain complexed with Beta-2 Microglobulin and a variant peptide, PA9, from the Human immunodeficiency virus (BaL) envelope glycoprotein 120 Deposited 2008-08-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 21–119（99 aa） Fragment：UNP residues 21 to 119
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；12% PEG 20000, 0.1M MES, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.41 Å R-free 0.271
3E6H MHC CLASS I H-2Dd heavy chain complexed with Beta-2 Microglobulin and a variant peptide, PI10, from the human immunodeficiency virus (BaL) envelope glycoprotein 120 Deposited 2008-08-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 21–119（99 aa） Fragment：EXTRACELLULAR DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；11% PEG20000,0.1M MES, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.10 Å R-free 0.250
3ECB Crystal structure of mouse H-2Dd in complex with peptide P18-I10 derived from human immunodeficiency virus envelope glycoprotein 120 Deposited 2008-08-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 21–119（99 aa） Fragment：UNP residues 21 to 119
Not recorded EDO 1,2-ETHANEDIOL × 6 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；16% PEG 3350, 0.2M Magnesium formate, , pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.70 Å R-free 0.227
3G08 Crystal structure of the alpha-galactosylceramide analog OCH in complex with mouse CD1d Deposited 2009-01-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 20–118（99 aa） Fragment：UNP residues 21-119
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 FEE N-{(1S,2S,3R)-1-[(alpha-D-galactopyranosyloxy)methyl]-2,3-dihydroxyoctyl}tetracosanamide × 1 PLM PALMITIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；16% polyethylene glycol 3350, 100mM Tris pH8.5, 2% tacsimate pH8.0 , VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.60 Å R-free 0.226
3GMM Structure of mouse CD1d in complex with C8Ph Deposited 2009-03-14 Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 21–119（99 aa） Fragment：UNP residues 21-119
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 C8P N-{(1S,2S,3R)-1-[(alpha-D-galactopyranosyloxy)methyl]-2,3-dihydroxyheptadecyl}-8-phenyloctanamide × 1 PLM PALMITIC ACID × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；295 K；0.2 M Malonate pH 4.5, 20%(v/v) PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.80 Å R-free 0.219
3GMN Structure of mouse CD1d in complex with C10Ph Deposited 2009-03-14 Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 21–119（99 aa） Fragment：UNP residues 21-119
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 C1Q N-{(1S,2S,3R)-1-[(alpha-D-galactopyranosyloxy)methyl]-2,3-dihydroxyheptadecyl}-10-phenyldecanamide × 1 PLM PALMITIC ACID × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；295 K；0.2 M Malonate pH 4.5, 20%(v/v) PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.70 Å R-free 0.218
3GMO Structure of mouse CD1d in complex with C8PhF Deposited 2009-03-14 Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 21–119（99 aa） Fragment：UNP residues 21-119
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 C8F 8-(4-fluorophenyl)-N-{(1S,2S,3R)-1-[(alpha-D-galactopyranosyloxy)methyl]-2,3-dihydroxyheptadecyl}octanamide × 1 PLM PALMITIC ACID × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；295 K；0.2 M Malonate pH 4.5, 20%(v/v) PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.60 Å R-free 0.216
3GMP Structure of mouse CD1d in complex with PBS-25 Deposited 2009-03-14 Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 21–119（99 aa） Fragment：UNP residues 21-119
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PBS (2S,3S,4R)-N-OCTANOYL-1-[(ALPHA-D-GALACTOPYRANOSYL)OXY]-2-AMINO-OCTADECANE-3,4-DIOL × 1 PLM PALMITIC ACID × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；295 K；0.2 M Malonate pH 4.5, 20%(v/v) PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.70 Å R-free 0.216
3GMQ Structure of mouse CD1d expressed in SF9 cells, no ligand added Deposited 2009-03-14 Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 21–119（99 aa） Fragment：UNP residues 21-119
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PLM PALMITIC ACID × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；295 K；0.2 M Malonate pH 4.5, 20%(v/v) PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.80 Å R-free 0.231
3GMR Structure of mouse CD1d in complex with C8Ph, different space group Deposited 2009-03-14 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 21–119（99 aa） Fragment：UNP residues 21-119
Not recorded C8P N-{(1S,2S,3R)-1-[(alpha-D-galactopyranosyloxy)methyl]-2,3-dihydroxyheptadecyl}-8-phenyloctanamide × 1 PLM PALMITIC ACID × 1 EDO 1,2-ETHANEDIOL × 4 PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；295 K；0.2 M Malonate pH 4.5, 20%(v/v) PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.90 Å R-free 0.230
3ILP Structure of mCD1d with bound glycolipid BbGL-2f from Borrelia burgdorferi Deposited 2009-08-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 21–119（99 aa） Fragment：UNP residues 21-119
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 1L2 (2S)-3-(alpha-D-galactopyranosyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl (9Z,12Z)-octadeca-9,12-dienoate × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；295 K；20% polyethylene glycol 4000, 100mM sodium citrate, 10% n-propanol, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.85 Å R-free 0.233
3ILQ Structure of mCD1d with bound glycolipid BbGL-2c from Borrelia burgdorferi Deposited 2009-08-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 21–119（99 aa） Fragment：UNP residues 21-119
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 1O2 (2S)-3-(alpha-D-galactopyranosyloxy)-2-(hexadecanoyloxy)propyl (9Z)-octadec-9-enoate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；295 K；17% polyethylene glycol 3350, 150mM di-ammonium hydrogen citrate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 2.05 Å R-free 0.251
3MA7 Crystal structure of Cardiolipin bound to mouse CD1D Deposited 2010-03-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 21–119（99 aa） Fragment：UNP RESIDUES 21-119
Not recorded CD4 (2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate × 1 PLM PALMITIC ACID × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 20% POLYETHYLENE GLYCOL 4000, 300MM CALCIUM ACETATE, 6% ETHYLENE GLYCOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K
Resolution 2.29 Å R-free 0.273
3MA7 Crystal structure of Cardiolipin bound to mouse CD1D Deposited 2010-03-23 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 21–119（99 aa） Fragment：UNP RESIDUES 21-119
Not recorded CD4 (2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate × 1 PLM PALMITIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 20% POLYETHYLENE GLYCOL 4000, 300MM CALCIUM ACETATE, 6% ETHYLENE GLYCOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K
Resolution 2.29 Å R-free 0.273
3NWM Crystal structure of a single chain construct composed of MHC class I H-2Kd, beta-2microglobulin and a peptide which is an autoantigen for type 1 diabetes Deposited 2010-07-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 21–119（99 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；20% PEG 8K, TrisHCl pH 8.5, Vapor diffusion, Sitting drop, temperature 298K
Resolution 2.70 Å R-free 0.284
3QUX Structure of the mouse CD1d-alpha-C-GalCer-iNKT TCR complex Deposited 2011-02-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 21–119（99 aa） Fragment：UNP residues 21-119
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 QUX N-[(3S,4S,5R)-4,5-dihydroxy-1-[(2R,3R,4R,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]nonadecan-3-yl]hexacosanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；20% polyethylene glycol 3350, 8% tacsimate, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 2.91 Å R-free 0.252
3QUY Structure of the mouse CD1d-BnNH-GSL-1'-iNKT TCR complex Deposited 2011-02-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 21–119（99 aa） Fragment：UNP residues 21-119
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 QUY (2S,3R,4S,5R,6S)-6-[(2S,3S,4R)-2-(hexacosanoylamino)-3,4-dihydroxy-octadecoxy]-3,4,5-trihydroxy-N-(phenylmethyl)oxane-2-carboxamide × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；295 K；17% polyethylene glycol 4000, 0.1 M citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 2.25 Å R-free 0.231
3QUZ Structure of the mouse CD1d-NU-alpha-GalCer-iNKT TCR complex Deposited 2011-02-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 21–119（99 aa） Fragment：UNP residues 21-119
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 QUV N-[(2S,3S,4R)-1-({6-deoxy-6-[(naphthalen-1-ylcarbamoyl)amino]-alpha-D-galactopyranosyl}oxy)-3,4-dihydroxyoctadecan-2-yl]hexacosanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；20% polyethylene glycole, 0.2 M ammonium citrate dibasic, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 2.30 Å R-free 0.233
3TN0 Structure of mouse Va14Vb8.2NKT TCR-mouse CD1d-a-C-Galactosylceramide complex Deposited 2011-09-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 21–119（99 aa） Fragment：UNP residues 21-119
Not recorded QUX N-[(3S,4S,5R)-4,5-dihydroxy-1-[(2R,3R,4R,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]nonadecan-3-yl]hexacosanamide × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；15-17% PEG 10K, 0.1M ammonium acetat, 0.1M BisTris pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 3.20 Å R-free 0.289
3TO4 Structure of mouse Valpha14Vbeta2-mouseCD1d-alpha-Galactosylceramide Deposited 2011-09-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 21–119（99 aa） Fragment：UNP residues 21-119
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；pH 5.5；295 K；17% PEG 10K, 0.1M ammonium acetate, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 3.10 Å R-free 0.268
4ELM Crystal structure of the mouse CD1d-lysosulfatide-Hy19.3 TCR complex Deposited 2012-04-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 21–119（99 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 SGF (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl 3-O-sulfo-beta-D-galactopyranoside × 1 PLM PALMITIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；11% PEG4000, 4% tacsimate, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 3.48 Å R-free 0.265
4ELM Crystal structure of the mouse CD1d-lysosulfatide-Hy19.3 TCR complex Deposited 2012-04-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 21–119（99 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 SGF (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl 3-O-sulfo-beta-D-galactopyranoside × 1 PLM PALMITIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；11% PEG4000, 4% tacsimate, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 3.48 Å R-free 0.265

25 other PDB entries and 30 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q91XJ8_MOUSE
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–99； UniProt 21–119

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 3gml

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3gml
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3gml
Deposition date deposition_date2009-03-14
Structure title titleStructure of mouse CD1d in complex with C6Ph
Keywords keywords;CD1, NKT cell, glycolipid, antigen presentation, Cell membrane, Disulfide bond, Endosome, Glycoprotein, Immune response, Immunoglobulin domain, Innate immunity, Lysosome, Membrane, Transmembrane, MHC I, Secreted, Immune System ;; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier24.86 Å
Radius of gyration Rg (electron density) rg_electron23.78 Å
Forward intensity I(0) i034587200.00
Molecular weight molecular_weight45537.0 kDa
Excluded volume excluded_volume57095 ų
Envelope volume envelope_volume69374 ų
Hydration-shell volume shell_volume24578 ų
Envelope diameter envelope_diameter81.0 Å
Shell Rg shell_rg30.59 Å
Envelope Rg envelope_rg24.03 Å
Shape Rg shape_rg23.74 Å
Total Rg total_rg24.75 Å
Total atoms total_atoms3201
Residues n_residues367
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax78.3 Å
Rg (real space) rg_real24.85 Å
Rg uncertainty (real space) rg_real_error0.47 Å
I(0) (real space) i0_real3.4590e+07
I(0) uncertainty (real space) i0_real_error4.6750e+05
Rg (reciprocal space) rg_reciprocal24.86 Å
I(0) (reciprocal space) i0_reciprocal34590000.0000
Solution quality estimate total_estimate0.9049
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.3 Å
Skewness Skewness skewness0.318
Kurtosis Kurtosis kurtosis-0.420
Angular range angular_range— – 0.3200 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4802000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.940; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.948
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (9)

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7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd3gmla1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.19 — MHC antigen-recognition domain
Superfamily Superfamily superfamilyd.19.1 — MHC antigen-recognition domain
Family Family familyd.19.1.1 — MHC antigen-recognition domain
Domain ID domain_idd3gmla2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd3gmla3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3gmlb_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (3 domains)

Domain ID domain_id3gmlA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily10 — MHC class I-like antigen recognition-like
Domain ID domain_id3gmlA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3gmlB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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8. Citations (1)

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9. Files and Curves (10)