SAXSdb — 4ndm

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

T-cell gamma protein,T-cell receptor beta-2 chain C region

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	Insufficient information Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 136–264	Fragment：AB18.1 TCR gamma chain Mutation：S173C, C191A	Human nkt tcr alpha chain × 1 （Q6PJ56,K7N5M3）	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

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	A0A0G2JNG9_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 119–247； UniProt 136–264

T-cell gamma protein,T-cell receptor beta-2 chain C region

Homo sapiens

UniProt A2NUW5

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 19–133	Fragment：AB18.1 TCR gamma chain Mutation：S173C, C191A	Human nkt tcr alpha chain × 1 （Q6PJ56,K7N5M3）	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

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	A2NUW5_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–118； UniProt 19–133

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	Insufficient information Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 118–220	Fragment：AB18.1 TCR delta chain Mutation：T167C	T-cell gamma protein,T-cell receptor beta-2 chain C region × 1 （A2NUW5,A0A0G2JNG9）	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

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 4NDM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4ZAK Crystal structure of the mCD1d/DB06-1/iNKTCR ternary complex Deposited 2015-04-13	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 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification 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 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 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification Different oligomeric state 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 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 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 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 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 mutation/modification 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 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 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 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 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 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 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 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 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 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 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 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 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 mutation/modification 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
6PX6 HLA-TCR complex Deposited 2019-07-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 118–210（93 aa）	Not recorded	No recorded non-water small molecule	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
6R2L NYBR1-A2-SLSKILDTV Deposited 2019-03-18	Different construct Different mutation/modification 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 mutation/modification 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 mutation/modification 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 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 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	2
Chains and sequence ranges	Author chain B； PDBConstruct 133–235； UniProt 118–220

Human nkt tcr alpha chain

Homo sapiens

UniProt Q6PJ56

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 21–142	Fragment：AB18.1 TCR delta chain Mutation：T167C	T-cell gamma protein,T-cell receptor beta-2 chain C region × 1 （A2NUW5,A0A0G2JNG9）	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

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 4NDM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4MNG Structure of the DP10.7 TCR with CD1d-sulfatide Deposited 2013-09-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 21–142（122 aa） Fragment：Single chain of delta and gamma variable domains,Single chain of delta and gamma variable domains	Mutation：end of gamma sequence TLVV swapped with KLII	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CIS (15Z)-N-((1S,2R,3E)-2-HYDROXY-1-{[(3-O-SULFO-BETA-D-GALACTOPYRANOSYL)OXY]METHYL}HEPTADEC-3-ENYL)TETRACOS-15-ENAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；11% PEG 4000 5% isopropanol 2 mM glutathione reduced/oxidized 50 mM tri-sodium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 3.01 Å R-free 0.207
4MNG Structure of the DP10.7 TCR with CD1d-sulfatide Deposited 2013-09-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 21–142（122 aa） Fragment：Single chain of delta and gamma variable domains,Single chain of delta and gamma variable domains	Mutation：end of gamma sequence TLVV swapped with KLII	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CIS (15Z)-N-((1S,2R,3E)-2-HYDROXY-1-{[(3-O-SULFO-BETA-D-GALACTOPYRANOSYL)OXY]METHYL}HEPTADEC-3-ENYL)TETRACOS-15-ENAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；11% PEG 4000 5% isopropanol 2 mM glutathione reduced/oxidized 50 mM tri-sodium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 3.01 Å R-free 0.207
4MNH Structure of the DP10.7 TCR Deposited 2013-09-10	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 21–126（106 aa） Fragment：DP10.7 TCR delta variable domain fused with human TCR alpha constant domain	Mutation：T167C	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；292 K；0.1 M Tris pH 8.5, 20% PEG 10k, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 3.30 Å R-free 0.285
4MNH Structure of the DP10.7 TCR Deposited 2013-09-10	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 21–126（106 aa） Fragment：DP10.7 TCR delta variable domain fused with human TCR alpha constant domain	Mutation：T167C	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；292 K；0.1 M Tris pH 8.5, 20% PEG 10k, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 3.30 Å R-free 0.285
6D7G Structure of 5F3 TCR in complex with HLA-A2/MART-1 Deposited 2018-04-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 21–115（95 aa） Chain D 127–253（127 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295.15 K；PEG 550 MME, TRIS, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K	Resolution 2.75 Å R-free 0.237
8ZA6 Cryo-EM structure of the gdTCR-CD3 complex Deposited 2024-04-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain m 1–114（114 aa） Chain m 127–296（170 aa）	Not recorded	CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.43 Å
8ZD4 Cryo-EM structure of the gdTCR-ECD Deposited 2024-05-01	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 22–114（93 aa） Chain A 128–229（102 aa） Chain D 22–114（93 aa） Chain D 128–229（102 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 2.90 Å
9LSY Structure of the gdTCR-Fab complex Deposited 2025-02-05	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 22–114（93 aa） Chain A 127–229（103 aa） Chain D 22–114（93 aa） Chain D 127–229（103 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.23 Å

6 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q6PJ56_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 12–131； UniProt 21–142

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	4ndm
Deposition date deposition_date	2013-10-27
Structure title title	Structure of the AB18.1 TCR
Keywords keywords	;Immunoglobulin, Histocompatibility antigens, T cell receptor, Immunological, lymphocytes, T cell recognition, activation, gamma delta T cell, Human, intraepithelial lymphocytes, CD1d, glycolipids, non-classical MHC, Glycoproteins, Cell-surface receptors, 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	25.49 Å
Radius of gyration Rg (electron density) rg_electron	24.52 Å
Forward intensity I(0) i0	40385200.00
Molecular weight molecular_weight	48639.0 kDa
Excluded volume excluded_volume	60610 Å³
Envelope volume envelope_volume	77731 Å³
Hydration-shell volume shell_volume	26497 Å³
Envelope diameter envelope_diameter	85.5 Å
Shell Rg shell_rg	31.64 Å
Envelope Rg envelope_rg	24.47 Å
Shape Rg shape_rg	24.55 Å
Total Rg total_rg	25.26 Å
Total atoms total_atoms	3438
Residues n_residues	446
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	82.2 Å
Rg (real space) rg_real	25.44 Å
Rg uncertainty (real space) rg_real_error	0.59 Å
I(0) (real space) i0_real	4.0390e+07
I(0) uncertainty (real space) i0_real_error	6.4110e+05
Rg (reciprocal space) rg_reciprocal	25.46 Å
I(0) (reciprocal space) i0_reciprocal	40390000.0000
Solution quality estimate total_estimate	0.9011
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.2 Å
Skewness Skewness skewness	0.241
Kurtosis Kurtosis kurtosis	-0.530
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	15780000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.922; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.949

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	T-cell gamma protein,T-cell receptor beta-2 chain C region
Molecular weight formula_weight	29324.7 kDa
Mutation mutation	S173C, C191A
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	3439

ADPSSNLEGGTKSVTRPTRSSAEITCDLTVINAFYIHWYLHQEGKAPQRLLYYDVSNSKDVLESGLSPGKYYTHTPRRWSWILILRNLIENDSGVYYCATWDRNNKKLFGSGTTLVVTEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRADSRGGLEVLFQ

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	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Human nkt tcr alpha chain
Molecular weight formula_weight	26382.4 kDa
Mutation mutation	T167C
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

ADLSQQGEEDPAQKVTQAQSSVSMPVRKAVTLNCLYETSWWSYYIFWYKQLPSKEMIFLIRQGSDEQNAKSGRYSVNFKKAAKSVALTISALQLEDSAKYFCALGDQILYWGLSHTDKLIFGKGTRVTVEPNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESSSRGGLEVLFQ

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	Trichoplusia ni

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1

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7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d4ndma1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d4ndma2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d4ndma3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4ndmb1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d4ndmb2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (4 domains)

Domain ID domain_id	4ndmA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4ndmA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4ndmB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4ndmB02
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	110.078 Å
Unit-cell length b length_b	142.213 Å
Unit-cell length c length_c	77.684 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	3.006 Å
Low-resolution limit resolution_low	43.539 Å
R factor r_factor	0.2441
R_work r_work	0.2424
R_free r_free	0.2797

fit	/app/data/saxs_computation/nd/4ndm/4ndm.fit
pddf	/app/data/pr_computation/nd/4ndm/4ndm.pr.out
profile	/app/data/saxs_computation/nd/4ndm/4ndm.dat

Structure of the AB18.1 TCR

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

T-cell gamma protein,T-cell receptor beta-2 chain C region

State in the Current Structure

Other States of the Same Protein in the Database

T-cell gamma protein,T-cell receptor beta-2 chain C region

State in the Current Structure

Other States of the Same Protein in the Database

Human nkt tcr alpha chain

State in the Current Structure

Other States of the Same Protein in the Database

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)