SAXSdb — 5u4y

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

IgG1 fc

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 Heteromer Protein × 4 其他Polymer 2 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 261–472 Chain B； UniProt 261–472	Fragment：unp residues 261-472	Immunoglobulin G-binding protein A × 2 ;beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；25% PEG 3400, 0.1M magnesium acetate, 0.1 M HEPES pH 7.0. Protein concentration 5mg/mL.	Resolution 2.50 Å R-free 0.230

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 5U4Y	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5NSC Fc DEKK heterodimer variant Deposited 2017-04-26	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 242–473（232 aa） Chain B 242–473（232 aa）	Mutation：L351K, T366K Mutation：L351D, L368E	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M sodium fluoride, 20% w/v PEG3350	Resolution 2.30 Å R-free 0.265
5NSG Fc DEDE homodimer variant Deposited 2017-04-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 242–473（232 aa）	Mutation：L351D, L368E	ZN ZINC ION × 6 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291 K；acetate buffer pH 4.5, 0.2 M zinc acetate, 16% w/v PEG 3000	Resolution 2.22 Å R-free 0.243
5U52 2 helix minimized version of the B-domain from Protein A (Z34C0 bound to IgG1 Fc (monoclinic form) Deposited 2016-12-06	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 262–469（208 aa） Fragment：unp residues 262-469 Chain B 262–469（208 aa） Fragment：unp residues 262-469	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；20% PEG monomethyl ether 550, 0.1M bis-tris propane pH 6.5, 0.1M NaCl, 5mg/mL protein concentration.	Resolution 1.94 Å R-free 0.228
5U66 Modified single helix from the B-domain of protein A bound to IgG1 Fc Deposited 2016-12-07	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 263–469（207 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；20% PEG 4000, 0.1M HEPES pH 7.2, 5mg/mL protein concentration.	Resolution 1.70 Å R-free 0.227
5VME Crystal structure of human IgG1 Fc K248E, T437R mutant Deposited 2017-04-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 251–473（223 aa） Chain B 251–473（223 aa）	Mutation：K248, T437R Mutation：K248, T437R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；35.5% PEG 300, 0.1 M HEPES, pH 7.0	Resolution 3.10 Å R-free 0.285
6CHF Crystal structure of a Fc fragment LALA mutant (L234A, L235A) of human IgG1 (crystal form 1) Deposited 2018-02-22	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 260–473（214 aa） Chain B 260–473（214 aa）	Mutation：L234A L235A Mutation：L234A L235A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；20% PEG MME 5,000 0.1 M Bis-Tris pH 6.5	Resolution 2.40 Å R-free 0.273
6CJC CRYSTAL STRUCTURE OF A FC FRAGMENT LALA MUTANT (L234A, L235A) OF HUMAN IGG1 (CRYSTAL FORM 3) Deposited 2018-02-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 260–473（214 aa） Chain B 260–473（214 aa）	Mutation：L234A, L235A Mutation：L234A, L235A	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；20% PEG MME 5,000 0.1 M Bis-Tris. pH 6.5	Resolution 2.58 Å R-free 0.241
6CJX Crystal structure of a Fc fragment LALA mutant (L234A, L235A) of human IgG1 (crystal form 2) Deposited 2018-02-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 260–473（214 aa） Chain B 260–473（214 aa）	Mutation：L234A, L235A Mutation：L234A, L235A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；25% PEG 3,350 0.1 M Bus-Tris pH 6.5	Resolution 2.44 Å R-free 0.264
6N9T Structure of a peptide-based photo-affinity cross-linker with Herceptin Fc Deposited 2018-12-04	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 249–472（224 aa） Fragment：residues 249-472	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；291 K；100mM sodium acetate pH=5.6, 12%(w/v) PEG 1000	Resolution 2.58 Å R-free 0.265
6N9T Structure of a peptide-based photo-affinity cross-linker with Herceptin Fc Deposited 2018-12-04	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 249–472（224 aa） Fragment：residues 249-472	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；291 K；100mM sodium acetate pH=5.6, 12%(w/v) PEG 1000	Resolution 2.58 Å R-free 0.265
6P6D HUMAN IGG1 FC FRAGMENT, C239 INSERTION MUTANT Deposited 2019-06-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 247–473（227 aa） Chain B 247–473（227 aa）	Mutation：C239 insertion Mutation：C239 insertion	CYS CYSTEINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；12 mg/mL protein, 20% w/v PEG 3350, 200 mM K Acetate	Resolution 2.31 Å R-free 0.268
7LF5 Structure of Hyperglycosylated Human IgG1 Fc (Fc267) Deposited 2021-01-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 242–473（232 aa）	Not recorded	FUC alpha-L-fucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；CRYSTALS GROWN BY MIXING 1 UL OF FC267 (10 MG/ML IN 10mM HEPES, 75mM NaCl pH 7.4) WITH 1 UL OF PRECIPITANT SOLUTION CONSISTING OF 0.1M HEPES pH 6.5, 8% w/v PEG6000	Resolution 2.60 Å R-free 0.243
7LF9 Structure of Hyperglycosylated Human IgG1 Fc (Fc329) Deposited 2021-01-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 242–473（232 aa） Chain B 242–473（232 aa）	Not recorded	FUC alpha-L-fucopyranose × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；CRYSTALS GROWN BY MIXING 1 UL OF FC329 (10 MG/ML IN 10mM HEPES, 75mM NaCl pH 7.4) WITH 1 UL OF PRECIPITANT SOLUTION CONSISTING OF 0.1M HEPES pH 6.5, 12.571% w/v PEG6000	Resolution 2.20 Å R-free 0.246
7LFN Structure of Hyperglycosylated Human IgG1 Fc (Fc267_329) Deposited 2021-01-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 242–473（232 aa） Chain B 242–473（232 aa）	Not recorded	FUC alpha-L-fucopyranose × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；CRYSTALS GROWN BY MIXING 1 UL OF FC267_329 (10 MG/ML IN 10mM HEPES, 75mM NaCl pH 7.4) WITH 1 UL OF PRECIPITANT SOLUTION CONSISTING OF 0.025M MES pH 7.0, 0.1M KCl, 20.571% w/v PEG3350	Resolution 2.60 Å R-free 0.270
7RHO Human IgG1 Fc fragment, hinge-free, expressed in E. coli Deposited 2021-07-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 263–473（211 aa） Fragment：engineered variant Chain B 263–473（211 aa） Fragment：engineered variant	Not recorded	EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；295 K；20% (w/v) PEG 6000, 40 mM CaCl2, 100 mM NaHepes	Resolution 2.00 Å R-free 0.270
7RHO Human IgG1 Fc fragment, hinge-free, expressed in E. coli Deposited 2021-07-18	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain D 263–473（211 aa） Fragment：engineered variant Chain E 263–473（211 aa） Fragment：engineered variant	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；295 K；20% (w/v) PEG 6000, 40 mM CaCl2, 100 mM NaHepes	Resolution 2.00 Å R-free 0.270
7RHO Human IgG1 Fc fragment, hinge-free, expressed in E. coli Deposited 2021-07-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain F 263–473（211 aa） Fragment：engineered variant Chain G 263–473（211 aa） Fragment：engineered variant	Not recorded	EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；295 K；20% (w/v) PEG 6000, 40 mM CaCl2, 100 mM NaHepes	Resolution 2.00 Å R-free 0.270
7RHO Human IgG1 Fc fragment, hinge-free, expressed in E. coli Deposited 2021-07-18	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain J 263–473（211 aa） Fragment：engineered variant Chain K 263–473（211 aa） Fragment：engineered variant	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；295 K；20% (w/v) PEG 6000, 40 mM CaCl2, 100 mM NaHepes	Resolution 2.00 Å R-free 0.270
8F8W Crystal structure of Nb.X0 bound to the afucosylated human IgG1 fragment crystal form I Deposited 2022-11-22	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 247–470（224 aa） Chain B 247–470（224 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Sodium HEPES 7.5 20 % w/v PEG 8000. Cryopreserved with 12.5% glycerol.	Resolution 2.71 Å R-free 0.241
8F8W Crystal structure of Nb.X0 bound to the afucosylated human IgG1 fragment crystal form I Deposited 2022-11-22	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 247–470（224 aa） Chain F 247–470（224 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Sodium HEPES 7.5 20 % w/v PEG 8000. Cryopreserved with 12.5% glycerol.	Resolution 2.71 Å R-free 0.241
8F8X Crystal structure of Nb.X0 bound to the afucosylated human IgG1 fragment crystal form II Deposited 2022-11-22	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 247–470（224 aa） Chain B 247–470（224 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20 % w/v PEG 6000, 0.1 M Sodium citrate 4.0, 0.2 M Lithium chloride. No additional cryoprotectant.	Resolution 2.60 Å R-free 0.285
8Q5U Endoglycosidase S2 in complex with IgG1 Fc Deposited 2023-08-09	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 247–473（227 aa） Chain B 247–473（227 aa） Chain C 247–473（227 aa）	Mutation：L234C E382A Mutation：L234C E382A Mutation：L234C E382A	GOL GLYCEROL × 4 PGE TRIETHYLENE GLYCOL × 5 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；Morpheus (Molecular Dimensions) conditon G12: 0.1 M carboxylic acids(0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Potassium sodium tartrate tetrahydrate; 0.2M Sodium oxamate); 0.1 M buffer system 3(Tris (base); BICINE); pH 8.5; 37.5 v/v Precipitant Mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350)	Resolution 3.00 Å R-free 0.252
9IUJ Integrin alpha-v beta-3 in complex with rhodostomin Deposited 2024-07-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 247–473（227 aa） Chain B 247–473（227 aa）	Not recorded	CA CALCIUM ION × 7 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.78 Å
9JEI Integrin alpha-v beta-3 in complex with Echistatin Deposited 2024-09-03	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 247–473（227 aa） Chain B 247–473（227 aa）	Not recorded	CA CALCIUM ION × 7 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.16 Å
9LT3 Integrin alpha-v beta-3 in complex with Trimucrin Deposited 2025-02-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 247–473（227 aa） Chain B 247–473（227 aa）	Not recorded	CA CALCIUM ION × 7 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.79 Å

20 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q6MZV7_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–212； UniProt 261–472 Author chain B； PDBConstruct 1–212； UniProt 261–472

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	5u4y
Deposition date deposition_date	2016-12-06
Structure title title	IgG Fc bound to 3 helix of the B-domain from Protein A
Keywords keywords	IgG1, Fc, helix, B-domain, Protein A, TRANSCRIPTION; TRANSCRIPTION
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	29.42 Å
Radius of gyration Rg (electron density) rg_electron	28.30 Å
Forward intensity I(0) i0	63794000.00
Molecular weight molecular_weight	62470.0 kDa
Excluded volume excluded_volume	78098 Å³
Envelope volume envelope_volume	101740 Å³
Hydration-shell volume shell_volume	30242 Å³
Envelope diameter envelope_diameter	99.8 Å
Shell Rg shell_rg	35.43 Å
Envelope Rg envelope_rg	27.89 Å
Shape Rg shape_rg	28.31 Å
Total Rg total_rg	28.99 Å
Total atoms total_atoms	4399
Residues n_residues	527
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	94.8 Å
Rg (real space) rg_real	29.35 Å
Rg uncertainty (real space) rg_real_error	0.72 Å
I(0) (real space) i0_real	6.3790e+07
I(0) uncertainty (real space) i0_real_error	9.2320e+05
Rg (reciprocal space) rg_reciprocal	29.38 Å
I(0) (reciprocal space) i0_reciprocal	63800000.0000
Solution quality estimate total_estimate	0.9004
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	40.4 Å
Skewness Skewness skewness	0.190
Kurtosis Kurtosis kurtosis	-0.424
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7766000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.917; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.951

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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	IgG1 fc
Molecular weight formula_weight	23991.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4537

LGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPG

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	Cricetulus griseus

Entity 2 Entity 2 polymer

Description description	Immunoglobulin G-binding protein A
Molecular weight formula_weight	6322.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

MKFNKEQQNAFYEILHLPNLNEEQRNAFIQSLKDDPSQSANLLAEAKKLNDAQAP

来源 Source

来源生物 organism	Staphylococcus aureus
NCBI Class编号 ncbi_taxonomy_id	1280
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 branched

Description description	;beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	1422.3 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 branched

Description description	;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	1260.2 kDa
Source method src_method	man
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	130

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5u4yc_
Class class	a — All alpha proteins
Fold Fold fold	a.8 — immunoglobulin/albumin-binding domain-like
Superfamily Superfamily superfamily	a.8.1 — Bacterial immunoglobulin/albumin-binding domains
Family Family family	a.8.1.1 — Immunoglobulin-binding protein A modules

Domain ID domain_id	d5u4yd_
Class class	a — All alpha proteins
Fold Fold fold	a.8 — immunoglobulin/albumin-binding domain-like
Superfamily Superfamily superfamily	a.8.1 — Bacterial immunoglobulin/albumin-binding domains
Family Family family	a.8.1.1 — Immunoglobulin-binding protein A modules

CATH v4.4 (6 domains)

Domain ID domain_id	5u4yA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5u4yA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5u4yB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5u4yB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5u4yC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	420 — Immunoglobulin FC, subunit C

Domain ID domain_id	5u4yD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	420 — Immunoglobulin FC, subunit C

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8. Citations (2)

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Unit-cell length a length_a	105.950 Å
Unit-cell length b length_b	152.260 Å
Unit-cell length c length_c	46.600 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	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.499 Å
Low-resolution limit resolution_low	41.075 Å
R factor r_factor	0.1949
R_work r_work	0.1931
R_free r_free	0.2301

fit	/app/data/saxs_computation/u4/5u4y/5u4y.fit
pddf	/app/data/pr_computation/u4/5u4y/5u4y.pr.out
profile	/app/data/saxs_computation/u4/5u4y/5u4y.dat

IgG Fc bound to 3 helix of the B-domain from Protein A

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

IgG1 fc

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

CATH v4.4 (6 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)