SAXSdb — 6px6

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1. Protein Identity and Related Structures Protein Identity & Related Structures

HLA class II histocompatibility antigen DQ alpha chain

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain A； UniProt 1–254	Not recorded	HLA class II histocompatibility antigen DQ beta chain × 1 （A0A0U5IHY9） DQ2.2-glut-L1 × 1 T-cell receptor, T1005.2.56, alpha chain,Human nkt tcr alpha chain × 1 （K7N5M3） T-cell receptor, T1005.2.56, beta chain × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；0.1 M MOPS/HEPES, pH 7.5, 12.5% v/v PEG1000, 12.5% v/v MPD, 12.5% w/v PEG3350, 0.04 M NPS mixture	Resolution 3.00 Å R-free 0.257

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 6PX6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6PY2 HLA-TCR complex Deposited 2019-07-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–254（254 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M MES, pH 6.5, 5% v/v MPD, 15% w/v PEG6000	Resolution 2.83 Å R-free 0.244
9EJI Peptide-independent T cell receptor recognition of HLA-DQ2 Deposited 2024-11-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 24–206（183 aa）	Not recorded	GOL GLYCEROL × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ACT ACETATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；8% Tacsimate pH 8.0, 20-24% w/v PEG3350	Resolution 2.20 Å R-free 0.220

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q08AS3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–254； UniProt 1–254

HLA class II histocompatibility antigen DQ beta chain

Homo sapiens

UniProt A0A0U5IHY9

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain B； UniProt 1–261	Not recorded	HLA class II histocompatibility antigen DQ alpha chain × 1 （Q08AS3） DQ2.2-glut-L1 × 1 T-cell receptor, T1005.2.56, alpha chain,Human nkt tcr alpha chain × 1 （K7N5M3） T-cell receptor, T1005.2.56, beta chain × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；0.1 M MOPS/HEPES, pH 7.5, 12.5% v/v PEG1000, 12.5% v/v MPD, 12.5% w/v PEG3350, 0.04 M NPS mixture	Resolution 3.00 Å R-free 0.257

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 6PX6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6PY2 HLA-TCR complex Deposited 2019-07-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–261（261 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M MES, pH 6.5, 5% v/v MPD, 15% w/v PEG6000	Resolution 2.83 Å R-free 0.244
9EJI Peptide-independent T cell receptor recognition of HLA-DQ2 Deposited 2024-11-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 33–228（196 aa）	Not recorded	GOL GLYCEROL × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ACT ACETATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；8% Tacsimate pH 8.0, 20-24% w/v PEG3350	Resolution 2.20 Å R-free 0.220

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A0U5IHY9_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–261； UniProt 1–261

T-cell receptor, T1005.2.56, alpha chain,Human nkt tcr alpha chain

Homo sapiens

UniProt K7N5M3

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain D； UniProt 118–210	Not recorded	HLA class II histocompatibility antigen DQ alpha chain × 1 （Q08AS3） HLA class II histocompatibility antigen DQ beta chain × 1 （A0A0U5IHY9） DQ2.2-glut-L1 × 1 T-cell receptor, T1005.2.56, beta chain × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；0.1 M MOPS/HEPES, pH 7.5, 12.5% v/v PEG1000, 12.5% v/v MPD, 12.5% w/v PEG3350, 0.04 M NPS mixture	Resolution 3.00 Å R-free 0.257

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 6PX6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4NDM Structure of the AB18.1 TCR Deposited 2013-10-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 118–220（103 aa） Fragment：AB18.1 TCR delta chain	Mutation：T167C	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；20% PEG3350, 0.2 M trisodium citrate, 2% Ethylene Glycol, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 3.01 Å R-free 0.280
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 C 116–210（95 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
5E6I Crystal structure of TCR PF8 in complex with flu MP(58-66) epitope presented by HLA-A2 Deposited 2015-10-09	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain G 116–210（95 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M immidazole pH8, 0.2M calcium acetate, 10%(v/v) PEG8000	Resolution 4.00 Å R-free 0.338
5E6I Crystal structure of TCR PF8 in complex with flu MP(58-66) epitope presented by HLA-A2 Deposited 2015-10-09	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 116–210（95 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M immidazole pH8, 0.2M calcium acetate, 10%(v/v) PEG8000	Resolution 4.00 Å R-free 0.338
5E6I Crystal structure of TCR PF8 in complex with flu MP(58-66) epitope presented by HLA-A2 Deposited 2015-10-09	Different construct Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain F 116–210（95 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M immidazole pH8, 0.2M calcium acetate, 10%(v/v) PEG8000	Resolution 4.00 Å R-free 0.338
5E6I Crystal structure of TCR PF8 in complex with flu MP(58-66) epitope presented by HLA-A2 Deposited 2015-10-09	Different construct Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain P 116–210（95 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M immidazole pH8, 0.2M calcium acetate, 10%(v/v) PEG8000	Resolution 4.00 Å R-free 0.338
5MEN Human Leukocyte Antigen A02 presenting ILAKFLHWL, in complex with cognate T-Cell Receptor Deposited 2016-11-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 118–206（89 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 5 GOL GLYCEROL × 1 SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M ammonium sulphate, 0.1M HEPES pH7, 20% PEG 8000	Resolution 2.81 Å R-free 0.272
5VCJ Structure of alpha-galactosylphytosphingosine bound by CD1d and in complex with the Va14Vb8.2 TCR Deposited 2017-03-31	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 C 116–210（95 aa） Fragment：UNP A0A0B4J1J9 residues 22-114,UNP K7N5M3 residues 116-210	Not recorded	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
5WLG Crystal Structure of H-2Db with the GAP501 peptide (SQL) Deposited 2017-07-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 118–194（77 aa）	Not recorded	NA SODIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.2；277 K；18%PEG3350, 2% ethylen glycol, 0.2M CaCl2, 0.1M HEPES pH 7.2	Resolution 2.10 Å R-free 0.249
5WLG Crystal Structure of H-2Db with the GAP501 peptide (SQL) Deposited 2017-07-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain I 118–194（77 aa）	Not recorded	NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.2；277 K；18%PEG3350, 2% ethylen glycol, 0.2M CaCl2, 0.1M HEPES pH 7.2	Resolution 2.10 Å R-free 0.249
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 C 96–210（115 aa）	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
6D78 The complex between high-affinity TCR DMF5(alpha-D26Y,beta-L98W) and human Class I MHC HLA-A2 with the bound MART-1(27-35)peptide Deposited 2018-04-24	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 118–206（89 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M Tris, 12% PEG6000, 0.2 M magnesium chloride	Resolution 2.35 Å R-free 0.255
6MIV Crystal structure of the mCD1d/xxq (JJ300)/iNKTCR ternary complex Deposited 2018-09-20	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 C 116–210（95 aa）	Not recorded	NA SODIUM ION × 3 GOL GLYCEROL × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 JU1 N-[(2S,3S,4R)-1-({4-O-[(4-tert-butylphenyl)methyl]-alpha-D-galactopyranosyl}oxy)-3,4-dihydroxyoctadecan-2-yl]hexacosanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；295 K；0.1 m sodium malonate pH 4.0, 12% PEG 3350	Resolution 2.05 Å R-free 0.219
6MIY Crystal structure of the mCD1d/xxa (JJ239)/iNKTCR ternary complex Deposited 2018-09-20	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 C 116–210（95 aa）	Not recorded	NA SODIUM ION × 2 CL CHLORIDE ION × 1 JTV N-{(2S,3S,4R)-1-[(4-O-benzyl-alpha-D-galactopyranosyl)oxy]-3,4-dihydroxyoctadecan-2-yl}hexacosanamide × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.2 m ammonium tartrate dibasic, 20% PEG 4000	Resolution 2.75 Å R-free 0.247
6MIY Crystal structure of the mCD1d/xxa (JJ239)/iNKTCR ternary complex Deposited 2018-09-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain G 116–210（95 aa）	Not recorded	NA SODIUM ION × 2 JTV N-{(2S,3S,4R)-1-[(4-O-benzyl-alpha-D-galactopyranosyl)oxy]-3,4-dihydroxyoctadecan-2-yl}hexacosanamide × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.2 m ammonium tartrate dibasic, 20% PEG 4000	Resolution 2.75 Å R-free 0.247
6MJ4 Crystal structure of MCD1D/INKTCR TERNARY COMPLEX bound to glycolipid (XXW) Deposited 2018-09-20	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 C 116–210（95 aa）	Not recorded	GOL GLYCEROL × 6 NA SODIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 JTG N-[(2S,3S,4R)-3,4-dihydroxy-1-{[4-O-(prop-2-en-1-yl)-alpha-D-galactopyranosyl]oxy}octadecan-2-yl]hexacosanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.1 m sodium malonate pH 4.0, 12% PEG 3350	Resolution 2.00 Å R-free 0.214
6MJ6 Crystal structure of the mCD1d/xxx (JJ166) /iNKTCR ternary complex Deposited 2018-09-20	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 C 116–210（95 aa）	Not recorded	GOL GLYCEROL × 7 NA SODIUM ION × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 JTM N-[(2S,3S,4R)-1-({4-O-[(4-chlorophenyl)methyl]-alpha-D-galactopyranosyl}oxy)-3,4-dihydroxyoctadecan-2-yl]hexacosanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.1 m sodium malonate pH 4.0, 12% PEG 3350	Resolution 2.45 Å R-free 0.234
6MJA Crystal structure of the mCD1d/xxo (JJ294) /iNKTCR ternary complex Deposited 2018-09-20	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 C 116–210（95 aa）	Not recorded	NA SODIUM ION × 2 GOL GLYCEROL × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 JTJ N-[(2S,3S,4R)-3,4-dihydroxy-1-({4-O-[(4-methylphenyl)methyl]-alpha-D-galactopyranosyl}oxy)octadecan-2-yl]hexacosanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.2 m ammonium tartrate dibasic, 20% PEG 4000	Resolution 2.35 Å R-free 0.237
6MJI Crystal structure of the mCD1d/xxs (JJ304) /iNKTCR ternary complex Deposited 2018-09-20	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 C 116–210（95 aa）	Not recorded	NA SODIUM ION × 2 GOL GLYCEROL × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 JTD N-[(2S,3S,4R)-1-{[4-O-(cyclopropylmethyl)-alpha-D-galactopyranosyl]oxy}-3,4-dihydroxyoctadecan-2-yl]hexacosanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.1 m sodium malonate pH 4.0, 12% PEG 3350	Resolution 2.30 Å R-free 0.227
6MJJ Crystal structure of the mCD1d/xxm (JJ290) /iNKTCR ternary complex Deposited 2018-09-21	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 C 116–210（95 aa）	Not recorded	GOL GLYCEROL × 10 NA SODIUM ION × 9 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 JU4 N-[(2S,3S,4R)-1-({4-O-[(3,4-dichlorophenyl)methyl]-alpha-D-galactopyranosyl}oxy)-3,4-dihydroxyoctadecan-2-yl]hexacosanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.1 m sodium malonate pH 4.0, 12% PEG 3350	Resolution 1.93 Å R-free 0.216
6MJQ Crystal structure of the mCD1d/xxp (JJ295) /iNKTCR ternary complex Deposited 2018-09-21	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 C 116–210（95 aa）	Not recorded	GOL GLYCEROL × 1 NA SODIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 JUD N-{(2S,3S,4R)-3,4-dihydroxy-1-[(4-O-{[4-(trifluoromethyl)phenyl]methyl}-alpha-D-galactopyranosyl)oxy]octadecan-2-yl}hexacosanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.1 m sodium malonate pH 4.0, 12% PEG 3350	Resolution 3.00 Å R-free 0.258
6MJQ Crystal structure of the mCD1d/xxp (JJ295) /iNKTCR ternary complex Deposited 2018-09-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain G 116–210（95 aa）	Not recorded	GOL GLYCEROL × 2 NA SODIUM ION × 2 JUD N-{(2S,3S,4R)-3,4-dihydroxy-1-[(4-O-{[4-(trifluoromethyl)phenyl]methyl}-alpha-D-galactopyranosyl)oxy]octadecan-2-yl}hexacosanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.1 m sodium malonate pH 4.0, 12% PEG 3350	Resolution 3.00 Å R-free 0.258
6R2L NYBR1-A2-SLSKILDTV Deposited 2019-03-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 118–198（81 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 2 GOL GLYCEROL × 3 SO4 SULFATE ION × 8 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；0.2 M NaCl, 0.1 M MES, 20% PEG 6000, pH 6.0 . Condition B07 from Molecular Dimensions PACT premier HT-96/FX-96, MD1-36	Resolution 2.30 Å R-free 0.265
6V80 Crystal structure of human CD1d presenting alpha-Galactosylceramide in complex with NKT12 TCR and VHH nanobody 1D12 Deposited 2019-12-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 96–210（115 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	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain H 96–210（115 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
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 C 116–210（95 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

19 other PDB entries and 26 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	K7N5M3_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 113–205； UniProt 118–210

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6px6
Deposition date deposition_date	2019-07-24
Structure title title	HLA-TCR complex
Keywords keywords	HLA, MHC, TCR, Complex, Celiac Disease, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	36.34 Å
Radius of gyration Rg (electron density) rg_electron	36.61 Å
Forward intensity I(0) i0	125539000.00
Molecular weight molecular_weight	88742.0 kDa
Excluded volume excluded_volume	110400 Å³
Envelope volume envelope_volume	148680 Å³
Hydration-shell volume shell_volume	37012 Å³
Envelope diameter envelope_diameter	139.5 Å
Shell Rg shell_rg	38.60 Å
Envelope Rg envelope_rg	37.09 Å
Shape Rg shape_rg	36.60 Å
Total Rg total_rg	36.79 Å
Total atoms total_atoms	6266
Residues n_residues	796
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	130.9 Å
Rg (real space) rg_real	36.86 Å
Rg uncertainty (real space) rg_real_error	1.24 Å
I(0) (real space) i0_real	1.2550e+08
I(0) uncertainty (real space) i0_real_error	1.9740e+06
Rg (reciprocal space) rg_reciprocal	36.54 Å
I(0) (reciprocal space) i0_reciprocal	125500000.0000
Solution quality estimate total_estimate	0.5613
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	32.7 Å
Skewness Skewness skewness	0.671
Kurtosis Kurtosis kurtosis	-0.058
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	16460000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.619; Stabil: 1.000; Sysdev: 0.028; Positv: 1.000; Valcen: 0.558; Smooth: 0.796

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	HLA class II histocompatibility antigen DQ alpha chain
Molecular weight formula_weight	27963.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	6291

MILNKALMLGALALTTVMSPCGGEDIVADHVASYGVNLYQSYGPSGQFTHEFDGDEEFYVDLERKETVWKLPLFHRLRFDPQFALTNIAVLKHNLNILIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDEPLLKHWEPEIPAPMSELTETVVCALGLSVGLVGIVVGTVLIIRGLRSVGASRHQGPL

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Baculovirus expression vector pFastBac1-HM

Entity 2 Entity 2 polymer

Description description	HLA class II histocompatibility antigen DQ beta chain
Molecular weight formula_weight	29714.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MSWKKALRIPGGLRAATVTLMLSMLSTPVAEGRDSPEDFVYQFKGMCYFTNGTERVRLVSRSIYNREEIVRFDSDVGEFRAVTLLGLPAAEYWNSQKDILERKRAAVDRVCRHNYQLELRTTLQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNGQEETAGVVSTPLIRNGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQSPITVEWRAQSESAQSKMLSGIGGFVLGLIFLGLGLIIHHRSQKGLLH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Baculovirus expression vector pFastBac1-HM

Entity 3 Entity 3 polymer

Description description	DQ2.2-glut-L1
Molecular weight formula_weight	1301.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

APFSEQEQPVLG

Entity 4 Entity 4 polymer

Description description	T-cell receptor, T1005.2.56, alpha chain,Human nkt tcr alpha chain
Molecular weight formula_weight	23798.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MKQEVTQIPAALSVPEGENLVLNCSFTDSAIYNLQWFRQDPGKGLTSLLLIQSSQREQTSGRLNASLDKSSGRSTLYIAASQPGDSATYLCAVHTGARLMFGDGTQLVVKPNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESSKLAAALEHHHHH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21

Entity 5 Entity 5 polymer

Description description	T-cell receptor, T1005.2.56, beta chain
Molecular weight formula_weight	28637.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MGVSQTPSNKVTEKGKYVELRCDPISGHTALYWYRQSLGQGPEFLIYFQGTGAADDSGLPNDRFFAVRPEGSVSTLKIQRTERGDSAVYLCASSHGASTDTQYFGPGTRLTVLEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRADKLAAALEHHHHHH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	25

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	6px6A01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily	10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1

Domain ID domain_id	6px6A02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6px6E01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	72.534 Å
Unit-cell length b length_b	99.416 Å
Unit-cell length c length_c	72.565 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	118.26 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	monoclinic

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	39.238 Å
R factor r_factor	0.2076
R_work r_work	0.2049
R_free r_free	0.2570

fit	/app/data/saxs_computation/px/6px6/6px6.fit
pddf	/app/data/pr_computation/px/6px6/6px6.pr.out
profile	/app/data/saxs_computation/px/6px6/6px6.dat

HLA-TCR complex

1. Protein Identity and Related Structures Protein Identity & Related Structures

HLA class II histocompatibility antigen DQ alpha chain

State in the Current Structure

Other States of the Same Protein in the Database

HLA class II histocompatibility antigen DQ beta chain

State in the Current Structure

Other States of the Same Protein in the Database

T-cell receptor, T1005.2.56, alpha chain,Human nkt tcr alpha chain

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 polymer

Polymer Polymer

来源 Source

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)