3h9y

Crystal structure of the IgE-Fc3-4 domains

Method: X-RAY DIFFRACTION D_max: 101.8 Å Quality: GOOD

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

Ig epsilon 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	Other combination Homooligomer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 209–428 Chain B； UniProt 209–428	Fragment：UNP residues 209-428 Mutation：N252Q, N264Q	;alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.3；293 K；1 microliter of protein at 10 mg/mL in 20 mM sodium chloride was added to 1 microliter well solution (100 mM ammonium acetate, 100 mM sodium acetate pH 4.6, 30% (w/v) PEG 4000) and mixed by pipetting., VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.23 Å R-free 0.262
2	Other combination Homooligomer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 209–428	Fragment：UNP residues 209-428 Mutation：N252Q, N264Q	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 NH4 AMMONIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.3；293 K；1 microliter of protein at 10 mg/mL in 20 mM sodium chloride was added to 1 microliter well solution (100 mM ammonium acetate, 100 mM sodium acetate pH 4.6, 30% (w/v) PEG 4000) and mixed by pipetting., VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.23 Å R-free 0.262

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 3H9Y	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1F6A Structure of the human ige-fc bound to its high affinity receptor fc(epsilon)ri(alpha) Deposited 2000-06-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 211–428（218 aa） Fragment：C(EPSILON)3-C(EPSILON)4 DOMAINS Chain D 211–428（218 aa） Fragment：C(EPSILON)3-C(EPSILON)4 DOMAINS	Not recorded	SO4 SULFATE ION × 5 CPS 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；296 K；Ammonium Sulfate, Tris, CHAPS, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 3.50 Å R-free 0.273
1FP5 CRYSTAL STRUCTURE ANALYSIS OF THE HUMAN IGE-FC CEPSILON3-CEPSILON4 FRAGMENT. Deposited 2000-08-30	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 357–574（218 aa） Fragment：CEPSILON3-CEPSILON4	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；295 K；PEG 4000, sodium acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.30 Å R-free 0.270
1G84 THE SOLUTION STRUCTURE OF THE C EPSILON2 DOMAIN FROM IGE Deposited 2000-11-16	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 106–210（105 aa） Fragment：C EPSILON2	Mutation：C16S, C104S	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 100mM；Pressure 1 NMR sample composition 2mM Ce2 U-15N,13C \| 90% H2O/10% D2O NMR sample composition 1.4mM Ce2 U-15N \| 90% H2O/10% D2O	Resolution not provided
2WQR The high resolution crystal structure of IgE Fc Deposited 2009-08-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 105–427（323 aa） Fragment：FC FRAGMENT, RESIDUES 105-427 Chain B 105–427（323 aa） Fragment：FC FRAGMENT, RESIDUES 105-427	Mutation：YES Mutation：YES	SO4 SULFATE ION × 4 GOL GLYCEROL × 2 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；291 K；THE PROTEIN CONCENTRATION WAS 1.9 MG/ML. CRYSTALS GREW AT 18 DEGREES C WITH 14% PEG 8000, 200MM LITHIUM SULPHATE, 100MM TRIS-HCL PH 8.5 AS PRECIPITANT.	Resolution 1.90 Å R-free 0.234
2Y7Q THE HIGH-AFFINITY COMPLEX BETWEEN IGE AND ITS RECEPTOR FC EPSILON RI Deposited 2011-02-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 104–428（325 aa） Fragment：FC FRAGMENT COMPRISING DOMAINS CEPSILON2-4, RESIDUES 104-427 Chain D 104–428（325 aa） Fragment：FC FRAGMENT COMPRISING DOMAINS CEPSILON2-4, RESIDUES 104-427	Mutation：YES Mutation：YES	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；SITTING DROP VAPOR DIFFUSION. RESERVOIR SOLUTION CONTAINED 2.8M SODIUM ACETATE PH 7.	Resolution 3.40 Å R-free 0.292
3H9Z Crystal structure of the IgE-Fc3-4 domains Deposited 2009-04-30	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 209–428（220 aa） Fragment：UNP residues 209-428 Chain B 209–428（220 aa） Fragment：UNP residues 209-428	Mutation：N252Q, N264Q Mutation：N252Q, N264Q	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；293 K；1 microliter of protein at 10 mg/mL in 20 mM sodium chloride was added to 1 microliter of well solution (100 mM ammonium acetate, 100 mM sodium acetate pH 4.6, 30% (w/v) PEG 4000) and mixed by pipetting., VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.45 Å R-free 0.277
3H9Z Crystal structure of the IgE-Fc3-4 domains Deposited 2009-04-30	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 209–428（220 aa） Fragment：UNP residues 209-428 Chain D 209–428（220 aa） Fragment：UNP residues 209-428	Mutation：N252Q, N264Q Mutation：N252Q, N264Q	NH4 AMMONIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；293 K；1 microliter of protein at 10 mg/mL in 20 mM sodium chloride was added to 1 microliter of well solution (100 mM ammonium acetate, 100 mM sodium acetate pH 4.6, 30% (w/v) PEG 4000) and mixed by pipetting., VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.45 Å R-free 0.277
3HA0 Crystal structure of the IgE-Fc3-4 domains Deposited 2009-04-30	Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 209–428（220 aa） Fragment：UNP residues 209-428 Chain B 209–428（220 aa） Fragment：UNP residues 209-428	Mutation：N252Q, N264Q Mutation：N252Q, N264Q	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；293 K；0.5 microliter of protein at 10 mg/mL in 20 mM sodium chloride was added to 0.5 microliter well solution (100 mM ammonium acetate, 100 mM sodium acetate pH 4.6, 30% (w/v) PEG 4000) and mixed by pipetting., VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.280
3HA0 Crystal structure of the IgE-Fc3-4 domains Deposited 2009-04-30	Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 209–428（220 aa） Fragment：UNP residues 209-428 Chain D 209–428（220 aa） Fragment：UNP residues 209-428	Mutation：N252Q, N264Q Mutation：N252Q, N264Q	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；293 K；0.5 microliter of protein at 10 mg/mL in 20 mM sodium chloride was added to 0.5 microliter well solution (100 mM ammonium acetate, 100 mM sodium acetate pH 4.6, 30% (w/v) PEG 4000) and mixed by pipetting., VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.280
3HA0 Crystal structure of the IgE-Fc3-4 domains Deposited 2009-04-30	Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 209–428（220 aa） Fragment：UNP residues 209-428 Chain F 209–428（220 aa） Fragment：UNP residues 209-428	Mutation：N252Q, N264Q Mutation：N252Q, N264Q	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；293 K；0.5 microliter of protein at 10 mg/mL in 20 mM sodium chloride was added to 0.5 microliter well solution (100 mM ammonium acetate, 100 mM sodium acetate pH 4.6, 30% (w/v) PEG 4000) and mixed by pipetting., VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.280
4EZM Crystal structure of the human IgE-Fc(epsilon)3-4 bound to its B cell receptor derCD23 Deposited 2012-05-03	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 209–428（220 aa） Fragment：Human IgE-Fc(epsilon)3-4, UNP residues 209-428 Chain B 209–428（220 aa） Fragment：Human IgE-Fc(epsilon)3-4, UNP residues 209-428	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；298 K；3% PEG 8,000, 0.1 M Tris-HCl pH 7.5, VAPOR DIFFUSION, temperature 298K	Resolution 3.10 Å R-free 0.283
4EZM Crystal structure of the human IgE-Fc(epsilon)3-4 bound to its B cell receptor derCD23 Deposited 2012-05-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 209–428（220 aa） Fragment：Human IgE-Fc(epsilon)3-4, UNP residues 209-428 Chain D 209–428（220 aa） Fragment：Human IgE-Fc(epsilon)3-4, UNP residues 209-428	Not recorded	MAN alpha-D-mannopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；298 K；3% PEG 8,000, 0.1 M Tris-HCl pH 7.5, VAPOR DIFFUSION, temperature 298K	Resolution 3.10 Å R-free 0.283
4EZM Crystal structure of the human IgE-Fc(epsilon)3-4 bound to its B cell receptor derCD23 Deposited 2012-05-03	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 209–428（220 aa） Fragment：Human IgE-Fc(epsilon)3-4, UNP residues 209-428 Chain F 209–428（220 aa） Fragment：Human IgE-Fc(epsilon)3-4, UNP residues 209-428	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；298 K；3% PEG 8,000, 0.1 M Tris-HCl pH 7.5, VAPOR DIFFUSION, temperature 298K	Resolution 3.10 Å R-free 0.283
4GKO Crystal structure of the calcium2+-bound human IgE-Fc(epsilon)3-4 bound to its B cell receptor derCD23 Deposited 2012-08-13	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 A 209–428（220 aa） Fragment：UNP residues 209-428 Chain B 209–428（220 aa） Fragment：UNP residues 209-428	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.2 M sodium acetate trihydrate, 0.1 M Tris pH 8.5, 16% PEG 4000, 10 mM CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 3.30 Å R-free 0.312
4GKO Crystal structure of the calcium2+-bound human IgE-Fc(epsilon)3-4 bound to its B cell receptor derCD23 Deposited 2012-08-13	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 209–428（220 aa） Fragment：UNP residues 209-428 Chain D 209–428（220 aa） Fragment：UNP residues 209-428	Not recorded	MAN alpha-D-mannopyranose × 2 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.2 M sodium acetate trihydrate, 0.1 M Tris pH 8.5, 16% PEG 4000, 10 mM CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 3.30 Å R-free 0.312
4GKO Crystal structure of the calcium2+-bound human IgE-Fc(epsilon)3-4 bound to its B cell receptor derCD23 Deposited 2012-08-13	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 209–428（220 aa） Fragment：UNP residues 209-428 Chain F 209–428（220 aa） Fragment：UNP residues 209-428	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.2 M sodium acetate trihydrate, 0.1 M Tris pH 8.5, 16% PEG 4000, 10 mM CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 3.30 Å R-free 0.312
4GRG Crystal structure of IgE complexed with E2_79, an anti-IgE inhibitor Deposited 2012-08-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 210–428（219 aa） Fragment：IG-LIKE DOMAINS 3 AND 4, RESIDUES 210-428 Chain D 210–428（219 aa） Fragment：IG-LIKE DOMAINS 3 AND 4, RESIDUES 210-428	Mutation：G216C Mutation：G216C	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；0.1 M Phosphate-citrate pH 4.2, 5% (w/v) PEG-3000, 25% (v/v) 1,2-propanediol, 10% (v/v) glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 4.24 Å R-free 0.338
4GT7 An engineered disulfide bond reversibly traps the IgE-Fc3-4 in a closed, non-receptor binding conformation Deposited 2012-08-28	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 210–426（217 aa） Fragment：IgE Fc Cepsilon3-Cepsilon4 fragment (unp residues 210-426) Chain B 210–426（217 aa） Fragment：IgE Fc Cepsilon3-Cepsilon4 fragment (unp residues 210-426)	Mutation：C328A, G335C Mutation：C328A, G335C	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；298 K；20 mM sodium acetate, pH 4.6, 28.8% (w/v) PEG 4000, 2% (w/v) Anapoe -X-405, VAPOR DIFFUSION, temperature 298K	Resolution 2.61 Å R-free 0.253
4GT7 An engineered disulfide bond reversibly traps the IgE-Fc3-4 in a closed, non-receptor binding conformation Deposited 2012-08-28	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 210–426（217 aa） Fragment：IgE Fc Cepsilon3-Cepsilon4 fragment (unp residues 210-426) Chain D 210–426（217 aa） Fragment：IgE Fc Cepsilon3-Cepsilon4 fragment (unp residues 210-426)	Mutation：C328A, G335C Mutation：C328A, G335C	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；298 K；20 mM sodium acetate, pH 4.6, 28.8% (w/v) PEG 4000, 2% (w/v) Anapoe -X-405, VAPOR DIFFUSION, temperature 298K	Resolution 2.61 Å R-free 0.253
4J4P The complex of human IgE-Fc with two bound Fab fragments Deposited 2013-02-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 105–427（323 aa） Chain B 105–427（323 aa）	Mutation：N265Q, N371Q Mutation：N265Q, N371Q	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；291 K；PEG 3350, sodium citrate, bis-tris propane, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.91 Å R-free 0.284
4KI1 Primitive triclinic crystal form of the human IgE-Fc(epsilon)3-4 bound to its B cell receptor derCD23 Deposited 2013-05-01	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 209–428（220 aa） Fragment：HUMAN IGE-FC(EPSILON)3-4, UNP residues 209-428 Chain B 209–428（220 aa） Fragment：HUMAN IGE-FC(EPSILON)3-4, UNP residues 209-428	Mutation：N252Q, N264Q Mutation：N252Q, N264Q	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；26 % (w/v) PEG 1,500 and 20 % (v/v) glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 3.20 Å R-free 0.266
4KI1 Primitive triclinic crystal form of the human IgE-Fc(epsilon)3-4 bound to its B cell receptor derCD23 Deposited 2013-05-01	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 209–428（220 aa） Fragment：HUMAN IGE-FC(EPSILON)3-4, UNP residues 209-428 Chain D 209–428（220 aa） Fragment：HUMAN IGE-FC(EPSILON)3-4, UNP residues 209-428	Mutation：N252Q, N264Q Mutation：N252Q, N264Q	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；26 % (w/v) PEG 1,500 and 20 % (v/v) glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 3.20 Å R-free 0.266
5ANM Crystal structure of IgE Fc in complex with a neutralizing antibody Deposited 2015-09-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain G 211–428（218 aa） Fragment：FC DOMAIN, CE3-CE4, RESIDUES 211-428	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 100 MM MGCL2, 100 MM SODIUM CITRATE PH 5.0 AND 15% PEG 4000	Resolution 2.85 Å R-free 0.260
5ANM Crystal structure of IgE Fc in complex with a neutralizing antibody Deposited 2015-09-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 211–428（218 aa） Fragment：FC DOMAIN, CE3-CE4, RESIDUES 211-428 Chain F 211–428（218 aa） Fragment：FC DOMAIN, CE3-CE4, RESIDUES 211-428	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 100 MM MGCL2, 100 MM SODIUM CITRATE PH 5.0 AND 15% PEG 4000	Resolution 2.85 Å R-free 0.260
5HYS Structure of IgE complexed with omalizumab Deposited 2016-02-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain G 209–428（220 aa） Fragment：Ig-like 3 and Ig-like 4 domains, residues 209-428 Chain I 209–428（220 aa） Fragment：Ig-like 3 and Ig-like 4 domains, residues 209-428	Mutation：C328A, G335C Mutation：C328A, G335C	SO4 SULFATE ION × 22	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；294 K；0.2M Lithium Sulfate, 0.1 M Tris pH 8.5, and 41% PEG 400	Resolution 2.50 Å R-free 0.239
5HYS Structure of IgE complexed with omalizumab Deposited 2016-02-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain J 209–428（220 aa） Fragment：Ig-like 3 and Ig-like 4 domains, residues 209-428 Chain K 209–428（220 aa） Fragment：Ig-like 3 and Ig-like 4 domains, residues 209-428	Mutation：C328A, G335C Mutation：C328A, G335C	SO4 SULFATE ION × 26	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；294 K；0.2M Lithium Sulfate, 0.1 M Tris pH 8.5, and 41% PEG 400	Resolution 2.50 Å R-free 0.239
5LGJ THE CRYSTAL STRUCTURE OF IGE FC MUTANT - P333C Deposited 2016-07-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 108–426（319 aa）	Not recorded	SO4 SULFATE ION × 3 PG4 TETRAETHYLENE GLYCOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；16% w/v PEG 8,000, 0.1M Tris-HCl pH 8.5, 0.2 M lithium sulfate	Resolution 2.60 Å R-free 0.248
5LGJ THE CRYSTAL STRUCTURE OF IGE FC MUTANT - P333C Deposited 2016-07-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 108–427（320 aa）	Not recorded	SO4 SULFATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；16% w/v PEG 8,000, 0.1M Tris-HCl pH 8.5, 0.2 M lithium sulfate	Resolution 2.60 Å R-free 0.248
5LGK Crystal structure of the human IgE-Fc bound to its B cell receptor derCD23 Deposited 2016-07-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 114–421（308 aa） Chain B 114–421（308 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；15% (w/v) PEG 8,000, 0.1 M sodium citrate, 0.05 M ammonium sulfate	Resolution 3.50 Å R-free 0.278
5LGK Crystal structure of the human IgE-Fc bound to its B cell receptor derCD23 Deposited 2016-07-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 114–421（308 aa） Chain D 114–421（308 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；15% (w/v) PEG 8,000, 0.1 M sodium citrate, 0.05 M ammonium sulfate	Resolution 3.50 Å R-free 0.278
5MOI Crystal structure of human IgE-Fc epsilon 3-4 Deposited 2016-12-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 209–428（220 aa） Chain B 209–428（220 aa） Chain C 209–428（220 aa） Chain D 209–428（220 aa） Chain E 209–428（220 aa） Chain F 209–428（220 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 6 PO4 PHOSPHATE ION × 6 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；25% (v/v) PEG1500, 0.1M SPG (succinic acid, sodium dihydrogen phosphate and glycine in the ratio 2:7:7)	Resolution 2.20 Å R-free 0.234
5MOJ Crystal structure of IgE-Fc epsilon 3-4 Deposited 2016-12-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 209–428（220 aa） Chain B 209–428（220 aa）	Not recorded	SO4 SULFATE ION × 7 EDO 1,2-ETHANEDIOL × 2 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；25% PEG 4000 0.15M Ammonium Sulphate 0.1M MES	Resolution 2.26 Å R-free 0.236
5MOK Crystal structure of human IgE-Fc epsilon 3-4 Deposited 2016-12-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 209–428（220 aa） Chain B 209–428（220 aa） Chain C 209–428（220 aa） Chain D 209–428（220 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 2 EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；25% (v/v) PEG1500 0.1M SPG (succinic acid, sodium dihydrogen phosphate and glycine in the ratio 2:7:7) at pH 6.0	Resolution 2.00 Å R-free 0.226
5MOL Human IgE-Fc crystal structure Deposited 2016-12-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 104–428（325 aa） Chain B 104–428（325 aa）	Not recorded	PG0 2-(2-METHOXYETHOXY)ETHANOL × 2 EDO 1,2-ETHANEDIOL × 5 PEG DI(HYDROXYETHYL)ETHER × 2 AE3 2-(2-ETHOXYETHOXY)ETHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M Tris HCL pH 8.5 25% PEG 550 MME	Resolution 1.75 Å R-free 0.232
5NQW IgE-Fc in complex with single domain antibody 026 Deposited 2017-04-21	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 A 215–426（212 aa） Chain B 215–426（212 aa）	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M imidazole pH 7.0 11-12 % polyethylene glycol 20.000	Resolution 3.40 Å R-free 0.241
6EYO Structure of extended IgE-Fc in complex with two anti-IgE Fabs Deposited 2017-11-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 104–428（325 aa） Chain B 104–428（325 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；0.1M Tris-HCl pH8.0 and 45% (v/v) pentaerythritol propoxylate (5/4PO/OH)	Resolution 3.70 Å R-free 0.288
6UQR Complex of IgE and Ligelizumab Deposited 2019-10-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 209–426（218 aa） Fragment：C3-4 Chain D 209–426（218 aa） Fragment：C3-4	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；287.15 K；0.2M Na Thiocyanate pH 6.9, 20% PEG3350, 10 mM Spermidine	Resolution 3.65 Å R-free 0.295
7MXI IgE-Fc in complex with DARPins E2_79 and E3_53 Deposited 2021-05-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 209–426（218 aa） Fragment：C3-4 Chain B 209–426（218 aa） Fragment：C3-4	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；291 K；E3_53, E2_79, and IgE-Fc3-4 were mixed in equimolar ratios with E3_53 and E2_79, and intact complexes were purified by SEC in 20 mM Tris-HCl, pH 8.0, 50mM NaCl and concentrated to 7mg/ml and mixed 1:1 with acetate buffer pH 4.6, 43% ethylene glycol w/v in hanging drops	Resolution 2.80 Å R-free 0.256
7SHT Structure of a partially disrupted IgE high affinity receptor complex bound to an omalizumab variant Deposited 2021-10-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric	Chain B 109–428（320 aa） Chain D 109–428（320 aa）	Mutation：G335C Mutation：G335C	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.29 Å
7SHU IgE-Fc in complex with omalizumab variant C02 Deposited 2021-10-11	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 B 209–426（218 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 EDO 1,2-ETHANEDIOL × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2M Lithium sulfate, 0.1 M Phosphate citrate pH 4.2, 20% (w/v) PEG 1000	Resolution 2.75 Å R-free 0.275
7SHU IgE-Fc in complex with omalizumab variant C02 Deposited 2021-10-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 209–426（218 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2M Lithium sulfate, 0.1 M Phosphate citrate pH 4.2, 20% (w/v) PEG 1000	Resolution 2.75 Å R-free 0.275
7SHY IgE-Fc in complex with omalizumab scFv Deposited 2021-10-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain G 209–426（218 aa） Fragment：C3-4 Chain H 209–426（218 aa） Fragment：C3-4	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MAN alpha-D-mannopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.02 M Magnesium chloride, 0.1M HEPES pH 7.5, 22% (w/v) Polyacrylic acid 5100 sodium salt	Resolution 3.00 Å R-free 0.230
7SHY IgE-Fc in complex with omalizumab scFv Deposited 2021-10-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 209–426（218 aa） Fragment：C3-4 Chain B 209–426（218 aa） Fragment：C3-4	Not recorded	GOL GLYCEROL × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.02 M Magnesium chloride, 0.1M HEPES pH 7.5, 22% (w/v) Polyacrylic acid 5100 sodium salt	Resolution 3.00 Å R-free 0.230
7SHZ IgE-Fc in complex with HAE Deposited 2021-10-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 209–426（218 aa） Fragment：C3-4 Chain B 209–426（218 aa） Fragment：C3-4	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PO4 PHOSPHATE ION × 2 ACT ACETATE ION × 1 EDO 1,2-ETHANEDIOL × 2 MAN alpha-D-mannopyranose × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Sodium acetate pH 4.6, 8% (w/v) PEG 4000	Resolution 3.00 Å R-free 0.235
7SHZ IgE-Fc in complex with HAE Deposited 2021-10-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain G 209–426（218 aa） Fragment：C3-4 Chain H 209–426（218 aa） Fragment：C3-4	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Sodium acetate pH 4.6, 8% (w/v) PEG 4000	Resolution 3.00 Å R-free 0.235
7SI0 IgE-Fc in complex with 813 Deposited 2021-10-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 209–426（218 aa） Fragment：C3-4 Chain B 209–426（218 aa） Fragment：C3-4	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M CAPS pH 10.5, 40%(v/v) MPD	Resolution 3.00 Å R-free 0.261
7SI0 IgE-Fc in complex with 813 Deposited 2021-10-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain G 209–426（218 aa） Fragment：C3-4 Chain H 209–426（218 aa） Fragment：C3-4	Not recorded	NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M CAPS pH 10.5, 40%(v/v) MPD	Resolution 3.00 Å R-free 0.261
8C1B Focused map for structure of IgE bound to the ectodomain of FceRIa Deposited 2022-12-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 108–423（316 aa） Chain X 108–423（316 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
8C1C Structure of IgE bound to the ectodomain of FceRIa Deposited 2022-12-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain H 1–423（423 aa） Chain X 1–423（423 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
8Z0T Structure of the human ige-fc bound to its high affinity receptor fc(epsilon) Deposited 2024-04-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 106–428（323 aa） Chain E 106–428（323 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.58 Å

33 other PDB entries and 50 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	IGHE_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–223； UniProt 209–428 Author chain B； PDBConstruct 4–223； UniProt 209–428 Author chain E； PDBConstruct 4–223； UniProt 209–428

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3h9y
Deposition date deposition_date	2009-04-30
Structure title title	Crystal structure of the IgE-Fc3-4 domains
Keywords keywords	;Immunoglobin, IgE, Fc, flexibility, hydrophobic pocket, Disulfide bond, Glycoprotein, Immunoglobulin C region, Immunoglobulin domain, 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	31.43 Å
Radius of gyration Rg (electron density) rg_electron	30.84 Å
Forward intensity I(0) i0	92347400.00
Molecular weight molecular_weight	73400.0 kDa
Excluded volume excluded_volume	91208 Å³
Envelope volume envelope_volume	126480 Å³
Hydration-shell volume shell_volume	35310 Å³
Envelope diameter envelope_diameter	107.4 Å
Shell Rg shell_rg	36.56 Å
Envelope Rg envelope_rg	30.38 Å
Shape Rg shape_rg	30.85 Å
Total Rg total_rg	31.38 Å
Total atoms total_atoms	5163
Residues n_residues	628
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	101.8 Å
Rg (real space) rg_real	31.44 Å
Rg uncertainty (real space) rg_real_error	0.80 Å
I(0) (real space) i0_real	9.2350e+07
I(0) uncertainty (real space) i0_real_error	1.5750e+06
Rg (reciprocal space) rg_reciprocal	31.44 Å
I(0) (reciprocal space) i0_reciprocal	92350000.0000
Solution quality estimate total_estimate	0.8800
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	36.7 Å
Skewness Skewness skewness	0.367
Kurtosis Kurtosis kurtosis	-0.229
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7324000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.894; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.755

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Ig epsilon chain C region
Molecular weight formula_weight	24920.1 kDa
Mutation mutation	N252Q, N264Q
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,E
Atom count atom_count	5410

ADPCADSNPRGVSAYLSRPSPFDLFIRKSPTITCLVVDLAPSKGTVQLTWSRASGKPVQHSTRKEEKQRNGTLTVTSTLPVGTRDWIEGETYQCRVTHPHLPRALMRSTTKTSGPRAAPEVYAFATPEWPGSRDKRTLACLIQNFMPEDISVQWLHNEVQLPDARHSTTQPRKTKGSGFFVFSRLEVTRAEWEQKDEFICRAVHEAASPSQTVQRAVSVNPGK

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 branched

Description description	;alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	1073.0 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 branched

Description description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	910.8 kDa
Source method src_method	man
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	AMMONIUM ION
Molecular weight formula_weight	18.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	247

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d3h9ya1
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	d3h9ya2
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	d3h9yb1
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	d3h9yb2
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	d3h9ye1
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	d3h9ye2
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 (6 domains)

Domain ID domain_id	3h9yA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3h9yA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3h9yB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3h9yB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3h9yE01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3h9yE02
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	153.676 Å
Unit-cell length b length_b	104.994 Å
Unit-cell length c length_c	49.222 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.61 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.230 Å
Low-resolution limit resolution_low	29.640 Å
R factor r_factor	0.2326
R_work r_work	0.2310
R_free r_free	0.2621

fit	/app/data/saxs_computation/h9/3h9y/3h9y.fit
pddf	/app/data/pr_computation/h9/3h9y/3h9y.pr.out
profile	/app/data/saxs_computation/h9/3h9y/3h9y.dat