SAXSdb — 3c2s

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

IGHM protein

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 256–480	Fragment：ANTIBODY FC FRAGMENT, residues 256-480 Mutation：L234F, L234E,P331S	;beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]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 ZN ZINC ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 8；298 K；5% PEG 3350, 200 mM Zn Acetate, 0.1 M Imidazole Malate, 5% Glycerol, pH 8.0, VAPOR DIFFUSION, temperature 298.0K	Resolution 2.30 Å R-free 0.275

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 3C2S	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1RHH Crystal Structure of the Broadly HIV-1 Neutralizing Fab X5 at 1.90 Angstrom Resolution Deposited 2003-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 25–256（232 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；PEG400, HEPES, 1,2-propanediol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 1.90 Å R-free 0.227
1RHH Crystal Structure of the Broadly HIV-1 Neutralizing Fab X5 at 1.90 Angstrom Resolution Deposited 2003-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 25–256（232 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；PEG400, HEPES, 1,2-propanediol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 1.90 Å R-free 0.227
2DD8 Crystal Structure of SARS-CoV Spike Receptor-Binding Domain Complexed with Neutralizing Antibody Deposited 2006-01-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 20–256（237 aa） Fragment：Fab m396, Heavy Chain	Not recorded	PO4 PHOSPHATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；15v/v% Glycerol, 20% PEG 6000, 100mM MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.30 Å R-free 0.261
2DD8 Crystal Structure of SARS-CoV Spike Receptor-Binding Domain Complexed with Neutralizing Antibody Deposited 2006-01-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 20–256（237 aa） Fragment：Fab m396, Heavy Chain	Not recorded	PO4 PHOSPHATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；15v/v% Glycerol, 20% PEG 6000, 100mM MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.30 Å R-free 0.261
2QL1 Structural Characterization of a Mutated, ADCC-Enhanced Human Fc Fragment Deposited 2007-07-12	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 256–480（225 aa） Fragment：Antibody Fc fragment	Not recorded	ZN ZINC ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；298 K；8% PEG 3350, 200 mM Zn Acetate, 5% Glycerol, 0.1 M Imidazole -Malate buffer, pH 8.0, VAPOR DIFFUSION, temperature 298.0K	Resolution 2.53 Å R-free 0.293

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

View Construct and Data Evidence

UniProt name	Q6PJF1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–225； UniProt 256–480

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	3c2s
Deposition date deposition_date	2008-01-25
Structure title title	Structural Characterization of a Human Fc Fragment Engineered for Lack of Effector Functions
Keywords keywords	Fc fragment, mutant, effector function, Receptor, PROTEIN BINDING, 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	23.26 Å
Radius of gyration Rg (electron density) rg_electron	22.47 Å
Forward intensity I(0) i0	11991100.00
Molecular weight molecular_weight	25642.0 kDa
Excluded volume excluded_volume	31897 Å³
Envelope volume envelope_volume	40829 Å³
Hydration-shell volume shell_volume	16341 Å³
Envelope diameter envelope_diameter	80.8 Å
Shell Rg shell_rg	27.61 Å
Envelope Rg envelope_rg	22.59 Å
Shape Rg shape_rg	22.47 Å
Total Rg total_rg	23.19 Å
Total atoms total_atoms	1789
Residues n_residues	210
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	79.7 Å
Rg (real space) rg_real	23.43 Å
Rg uncertainty (real space) rg_real_error	0.55 Å
I(0) (real space) i0_real	1.1990e+07
I(0) uncertainty (real space) i0_real_error	1.6160e+05
Rg (reciprocal space) rg_reciprocal	23.40 Å
I(0) (reciprocal space) i0_reciprocal	11990000.0000
Solution quality estimate total_estimate	0.8496
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	78.5 Å
Skewness Skewness skewness	0.445
Kurtosis Kurtosis kurtosis	-0.466
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2625000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.790; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.678; Smooth: 0.992

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	IGHM protein
Molecular weight formula_weight	25408.7 kDa
Mutation mutation	L234F, L234E,P331S
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1864

THTCPPCPAPEFEGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPASIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK

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	;beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]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	1625.5 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	75

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3c2sa1
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	d3c2sa2
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	3c2sA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3c2sA02
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	50.178 Å
Unit-cell length b length_b	147.301 Å
Unit-cell length c length_c	75.473 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2193
R_work r_work	0.2164
R_free r_free	0.2754

fit	/app/data/saxs_computation/c2/3c2s/3c2s.fit
pddf	/app/data/pr_computation/c2/3c2s/3c2s.pr.out
profile	/app/data/saxs_computation/c2/3c2s/3c2s.dat

Structural Characterization of a Human Fc Fragment Engineered for Lack of Effector Functions

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

IGHM protein

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