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Protein Structures and Oligomeric States

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

Current Protein Identity：K7N5M3 New Search
20PDB entries
27Biological assembly
27chain/assembly records
Main Difference Dimensions in This Set
Different construct Different mutation/modification Different assembly state Different ligand/ion Different experimental conditions Different structure-quality metrics

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

Related-Structure Differences

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

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method Experimental Conditions Structure Quality
4NDM Structure of the AB18.1 TCR Deposited 2013-10-27 Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
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 Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count
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 Assembly 3 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count
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 Assembly 4 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count
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 Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count
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 Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count
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 Assembly 2 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count
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 Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count
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 Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 2 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 2 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count
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 Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count
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 Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count
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 Assembly 2 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count
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 Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
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

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