SAXSdb — 6d58

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

Immunoglobulin heavy constant gamma 3

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 164–377 Chain B； UniProt 164–377	Not recorded	;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-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 ; × 2	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 2.39 Å R-free 0.286

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 6D58	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4WWI Crystal structure of the C domain of staphylococcal protein A in complex with the Fc fragment of human IgG at 2.3 Angstrom resolution Deposited 2014-11-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 168–377（210 aa） Fragment：UNP residues 168-377	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；NaOAc, ammonium sulfate, PEG 5K MME, glycerol	Resolution 2.31 Å R-free 0.251
4WWI Crystal structure of the C domain of staphylococcal protein A in complex with the Fc fragment of human IgG at 2.3 Angstrom resolution Deposited 2014-11-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 168–377（210 aa） Fragment：UNP residues 168-377	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；NaOAc, ammonium sulfate, PEG 5K MME, glycerol	Resolution 2.31 Å R-free 0.251
4WWI Crystal structure of the C domain of staphylococcal protein A in complex with the Fc fragment of human IgG at 2.3 Angstrom resolution Deposited 2014-11-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 168–377（210 aa） Fragment：UNP residues 168-377	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；NaOAc, ammonium sulfate, PEG 5K MME, glycerol	Resolution 2.31 Å R-free 0.251
4ZNC Fc fragment of human IgG in complex with the C domain of staphylococcal protein A mutant - Q9W Deposited 2015-05-04	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 168–377（210 aa） Fragment：UNP residues 168-377	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；298 K；PEG 5000 MME, ammonium sulfate, sodium acetate	Resolution 2.28 Å R-free 0.242
4ZNC Fc fragment of human IgG in complex with the C domain of staphylococcal protein A mutant - Q9W Deposited 2015-05-04	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 168–377（210 aa） Fragment：UNP residues 168-377	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；298 K；PEG 5000 MME, ammonium sulfate, sodium acetate	Resolution 2.28 Å R-free 0.242
4ZNC Fc fragment of human IgG in complex with the C domain of staphylococcal protein A mutant - Q9W Deposited 2015-05-04	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 168–377（210 aa） Fragment：UNP residues 168-377	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；298 K；PEG 5000 MME, ammonium sulfate, sodium acetate	Resolution 2.28 Å R-free 0.242
5M3V BEAT Fc Deposited 2016-10-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 271–377（107 aa）	Mutation：;S364K T366V K370T K392Y F405S Y407V K409W T411N,S364K T366V K370T K392Y F405S Y407V K409W T411N,S364K T366V K370T K392Y F405S Y407V K409W T411N,S364K T366V K370T K392Y F405S Y407V K409W T411N ; Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 10.2 MG/ML PROTEIN IN 10 MM TRIS-HCL PH8.0, 100 MM NACL, 1 MM EDTA, EQUALLY WITH 27.00 %(W/V) PEG 1500	Resolution 1.97 Å R-free 0.279
5W38 1.80A resolution structure of human IgG3 Fc (N392K) Deposited 2017-06-07	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 155–377（223 aa） Fragment：Fc domain, UNP residues 155-377 Chain B 155–377（223 aa） Fragment：Fc domain, UNP residues 155-377	Mutation：N392K Mutation：N392K	FLC CITRATE ANION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；20% (w/v) PEG 4000, 100 mM sodium citrate/citric acid, 10% (v/v) 2-propanol	Resolution 1.80 Å R-free 0.223
6G1E BEAT Fc with improved heterodimerization (Q3A-D84.4Q) Deposited 2018-03-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 161–377（217 aa）	Mutation：L234A, L235A, Q347A, S364K, T366V, K370T, N392Y, F405S, Y407V, K409W, T411N Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 12.0 MG/ML PROTEIN IN 10 MM HEPES PH8.0, 100 MM NACL, 1 MM EDTA, EQUALLY WITH 33.00 %(W/V) PEG 1500	Resolution 1.88 Å R-free 0.272

5 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	IGHG3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–214； UniProt 164–377 Author chain B； PDBConstruct 1–214； UniProt 164–377

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	6d58
Deposition date deposition_date	2018-04-19
Structure title title	Crystal structure of a Fc fragment of Human IgG3
Keywords keywords	IMMUNOGLOBULIN, IGG3, IMMUNE SYSTEM, IMMUNOGLOBULIN-LIKE BETA SANDWICH, FC FRAGMENT; 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	26.42 Å
Radius of gyration Rg (electron density) rg_electron	25.22 Å
Forward intensity I(0) i0	41439200.00
Molecular weight molecular_weight	50004.0 kDa
Excluded volume excluded_volume	62632 Å³
Envelope volume envelope_volume	80989 Å³
Hydration-shell volume shell_volume	26448 Å³
Envelope diameter envelope_diameter	79.0 Å
Shell Rg shell_rg	32.76 Å
Envelope Rg envelope_rg	24.78 Å
Shape Rg shape_rg	25.23 Å
Total Rg total_rg	26.06 Å
Total atoms total_atoms	3516
Residues n_residues	414
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	78.6 Å
Rg (real space) rg_real	26.27 Å
Rg uncertainty (real space) rg_real_error	0.45 Å
I(0) (real space) i0_real	4.1440e+07
I(0) uncertainty (real space) i0_real_error	6.2330e+05
Rg (reciprocal space) rg_reciprocal	26.32 Å
I(0) (reciprocal space) i0_reciprocal	41440000.0000
Solution quality estimate total_estimate	0.9163
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	36.7 Å
Skewness Skewness skewness	0.043
Kurtosis Kurtosis kurtosis	-0.665
Angular range angular_range	— – 0.3000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5476000.0000
Real-space data points n_real_points	61
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.980; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.970

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Immunoglobulin heavy constant gamma 3
Molecular weight formula_weight	24249.5 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	3538

LLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVQFKWYVDGVEVHNAKTKPREEQYNSTFRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKTKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESSGQPENNYNTTPPMLDSDGSFFLYSKLTVDKSRWQQGNIFSCSVMHEALHNHFTQKSLSLSPGK

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	Homo sapiens

Entity 2 Entity 2 branched

Description description	;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-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	1463.3 kDa
Source method src_method	man
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	22

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d6d58a1
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	d6d58a2
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	d6d58b1
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	d6d58b2
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 (2 domains)

Domain ID domain_id	6d58A02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6d58B02
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	49.590 Å
Unit-cell length b length_b	80.678 Å
Unit-cell length c length_c	136.029 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.390 Å
Low-resolution limit resolution_low	35.888 Å
R factor r_factor	0.2369
R_work r_work	0.2344
R_free r_free	0.2861

fit	/app/data/saxs_computation/d5/6d58/6d58.fit
pddf	/app/data/pr_computation/d5/6d58/6d58.pr.out
profile	/app/data/saxs_computation/d5/6d58/6d58.dat

Crystal structure of a Fc fragment of Human IgG3

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

Immunoglobulin heavy constant gamma 3

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