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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：Q9Y6Y9 New Search
6PDB entries
8Biological assembly
10chain/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
2E56 Crystal structure of human MD-2 Deposited 2006-12-19 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 17–160（144 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 MYR MYRISTIC ACID × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；277 K；20% PEG8000, 120mM Na-acetate,70mM Na-cacodylate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Resolution 2.00 Å R-free 0.249
2E59 Crystal structure of human MD-2 in complex with lipid IVa Deposited 2006-12-19 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 17–160（144 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 LP5 (R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-(HYDROXYMETHYL)-5-((R)-3-HYDROXYTETRADECANAMIDO)-6-(PHOSPHONOOXY)TETRAHYDRO-2H-PYRAN-4-YL) 3-HYDROXYTETRADECANOATE × 1 LP4 2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-4-O-phosphono-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；277 K；15% PEG3350, 40mM Na-citrate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Resolution 2.21 Å R-free 0.263
2Z65 Crystal structure of the human TLR4 TV3 hybrid-MD-2-Eritoran complex Deposited 2007-07-22 Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain C 19–158（140 aa）
Not recorded E55 3-O-DECYL-2-DEOXY-6-O-{2-DEOXY-3-O-[(3R)-3-METHOXYDECYL]-6-O-METHYL-2-[(11Z)-OCTADEC-11-ENOYLAMINO]-4-O-PHOSPHONO-BETA-D-GLUCOPYRANOSYL}-2-[(3-OXOTETRADECANOYL)AMINO]-1-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；296 K；0.2M Ammonium Sulfate, 0.1M Sodium Acetate, 20% PEG 4000, 5% Ethanol, pH 4.5, VAPOR DIFFUSION, temperature 296K
Resolution 2.70 Å R-free 0.289
2Z65 Crystal structure of the human TLR4 TV3 hybrid-MD-2-Eritoran complex Deposited 2007-07-22 Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain D 19–158（140 aa）
Not recorded E55 3-O-DECYL-2-DEOXY-6-O-{2-DEOXY-3-O-[(3R)-3-METHOXYDECYL]-6-O-METHYL-2-[(11Z)-OCTADEC-11-ENOYLAMINO]-4-O-PHOSPHONO-BETA-D-GLUCOPYRANOSYL}-2-[(3-OXOTETRADECANOYL)AMINO]-1-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；296 K；0.2M Ammonium Sulfate, 0.1M Sodium Acetate, 20% PEG 4000, 5% Ethanol, pH 4.5, VAPOR DIFFUSION, temperature 296K
Resolution 2.70 Å R-free 0.289
3FXI Crystal structure of the human TLR4-human MD-2-E.coli LPS Ra complex Deposited 2009-01-21 Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain C 19–160（142 aa）
Chain D 19–160（142 aa）
Not recorded FTT 3-HYDROXY-TETRADECANOIC ACID × 8 DAO LAURIC ACID × 2 MYR MYRISTIC ACID × 2 PO4 PHOSPHATE ION × 8 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；278 K；50mM MgCl2, 0.1M Na-HEPES pH 7.5, 30% PEG MME 550, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Resolution 3.10 Å R-free 0.281
3ULA Crystal structure of the TV3 mutant F63W-MD-2-Eritoran complex Deposited 2011-11-10 Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain D 19–158（140 aa） Fragment：UNP RESIDUES 19-158
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 E55 3-O-DECYL-2-DEOXY-6-O-{2-DEOXY-3-O-[(3R)-3-METHOXYDECYL]-6-O-METHYL-2-[(11Z)-OCTADEC-11-ENOYLAMINO]-4-O-PHOSPHONO-BETA-D-GLUCOPYRANOSYL}-2-[(3-OXOTETRADECANOYL)AMINO]-1-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；296 K；0.1M sodium acetate (pH4.5), 22% w/v PEG 8000, 0.2M lithium sulfate, VAPOR DIFFUSION, temperature 296K
Resolution 3.60 Å R-free 0.341
3ULA Crystal structure of the TV3 mutant F63W-MD-2-Eritoran complex Deposited 2011-11-10 Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain B 19–158（140 aa） Fragment：UNP RESIDUES 19-158
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 E55 3-O-DECYL-2-DEOXY-6-O-{2-DEOXY-3-O-[(3R)-3-METHOXYDECYL]-6-O-METHYL-2-[(11Z)-OCTADEC-11-ENOYLAMINO]-4-O-PHOSPHONO-BETA-D-GLUCOPYRANOSYL}-2-[(3-OXOTETRADECANOYL)AMINO]-1-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；296 K；0.1M sodium acetate (pH4.5), 22% w/v PEG 8000, 0.2M lithium sulfate, VAPOR DIFFUSION, temperature 296K
Resolution 3.60 Å R-free 0.341
4G8A Crystal structure of human TLR4 polymorphic variant D299G and T399I in complex with MD-2 and LPS Deposited 2012-07-23 Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain C 17–160（144 aa）
Chain D 17–160（144 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 LP4 2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-4-O-phosphono-beta-D-glucopyranose × 2 LP5 (R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-(HYDROXYMETHYL)-5-((R)-3-HYDROXYTETRADECANAMIDO)-6-(PHOSPHONOOXY)TETRAHYDRO-2H-PYRAN-4-YL) 3-HYDROXYTETRADECANOATE × 2 DAO LAURIC ACID × 2 MYR MYRISTIC ACID × 2 KDO 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；26-30% (w/v) PEG1000, 0.1M Tris-HCl (pH 8.0), VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.40 Å R-free 0.249

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.