SAXSdb — 5ea0

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

Complement factor H-related protein 2

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain P； UniProt 150–162	Fragment：UNP residues 150-162 Non-standard monomer：Yes (specific site not provided by mmCIF)	Heavy chain of antibody 7968 Fab fragment × 1 Light chain of antibody 7968 Fab fragment × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 3.5；293 K；Drop composed of Fab at 20 mg/ml mixed with 25 mM citric acid pH 3.5, 8% PEG 3350; over a reservoir of 24% PEG 3350	Resolution 2.00 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 5EA0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3ZD1 STRUCTURE OF THE TWO C-TERMINAL DOMAINS OF COMPLEMENT FACTOR H RELATED PROTEIN 2 Deposited 2012-11-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 147–270（124 aa） Fragment：SCR DOMAINS 3 AND 4, RESIDUES 147-270	Not recorded	EDO 1,2-ETHANEDIOL × 6	X-RAY DIFFRACTION X-ray crystallization conditions 30% (W/V) PEG 8000, 0.2M AMMONIUM SULPHATE	Resolution 2.00 Å R-free 0.240
3ZD1 STRUCTURE OF THE TWO C-TERMINAL DOMAINS OF COMPLEMENT FACTOR H RELATED PROTEIN 2 Deposited 2012-11-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 147–270（124 aa） Fragment：SCR DOMAINS 3 AND 4, RESIDUES 147-270	Not recorded	EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions 30% (W/V) PEG 8000, 0.2M AMMONIUM SULPHATE	Resolution 2.00 Å R-free 0.240
9N1Z Structure of C3d Bound to a Fragment of FHR-2 Deposited 2025-01-27	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 145–270（126 aa）	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.075 M HEPES [PH 7.5] 1.2 M Ammonium Sulfate	Resolution 2.31 Å R-free 0.227
9N1Z Structure of C3d Bound to a Fragment of FHR-2 Deposited 2025-01-27	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 145–270（126 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.075 M HEPES [PH 7.5] 1.2 M Ammonium Sulfate	Resolution 2.31 Å R-free 0.227
9N20 Structure of C3d Bound to a Fragment of FHR-2 and S. aureus Efb-C Deposited 2025-01-27	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 145–270（126 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M imidazole [pH 6.7] 12% (w/v) peg-20k	Resolution 3.30 Å R-free 0.214

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

View Construct and Data Evidence

UniProt name	FHR2_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain P； PDBConstruct 2–14； UniProt 150–162

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	5ea0
Deposition date deposition_date	2015-10-15
Structure title title	Structure of the antibody 7968 with human complement factor H-derived peptide
Keywords keywords	complement factor H CFH SCR19 SCR19-20, 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	25.17 Å
Radius of gyration Rg (electron density) rg_electron	24.27 Å
Forward intensity I(0) i0	39368900.00
Molecular weight molecular_weight	48015.0 kDa
Excluded volume excluded_volume	59811 Å³
Envelope volume envelope_volume	73046 Å³
Hydration-shell volume shell_volume	25433 Å³
Envelope diameter envelope_diameter	84.5 Å
Shell Rg shell_rg	31.21 Å
Envelope Rg envelope_rg	24.11 Å
Shape Rg shape_rg	24.26 Å
Total Rg total_rg	25.09 Å
Total atoms total_atoms	3380
Residues n_residues	432
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	81.6 Å
Rg (real space) rg_real	25.16 Å
Rg uncertainty (real space) rg_real_error	0.55 Å
I(0) (real space) i0_real	3.9370e+07
I(0) uncertainty (real space) i0_real_error	5.4840e+05
Rg (reciprocal space) rg_reciprocal	25.16 Å
I(0) (reciprocal space) i0_reciprocal	39370000.0000
Solution quality estimate total_estimate	0.9013
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.8 Å
Skewness Skewness skewness	0.314
Kurtosis Kurtosis kurtosis	-0.409
Angular range angular_range	— – 0.3150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7860000.0000
Real-space data points n_real_points	64
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: 0.972; Smooth: 0.989

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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	Heavy chain of antibody 7968 Fab fragment
Molecular weight formula_weight	23648.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H
Atom count atom_count	3721

EVQLVESGGGVVQPGRSLRLSCAASGFTFSRYGMHWVRQAPGKGLEWVAVMSYDGSTKYYADSVKGRFAISRDNPKNTLFLQMNSLRPDDTAVYYCAKGGAAAAVMDVWGKGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDK

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Light chain of antibody 7968 Fab fragment
Molecular weight formula_weight	24403.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

DIVMTQSPDSLTVSLGERATISCKSSQRLLYSSNNKNYLAWYQQKPGQPPKLLMYWASTRESGVPDRFSGSGSGTDFSLTISSLQAEDVAVYYCQQYYNPPWTFGQGTKVEVKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Complement factor H-related protein 2
Molecular weight formula_weight	1303.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

XGPPPPIDNGDITSX

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	341

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	5ea0H01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5ea0H02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5ea0L01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5ea0L02
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	51.280 Å
Unit-cell length b length_b	65.547 Å
Unit-cell length c length_c	71.267 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.37 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	38.009 Å
R factor r_factor	0.2017
R_work r_work	0.1959
R_free r_free	0.2753

fit	/app/data/saxs_computation/ea/5ea0/5ea0.fit
pddf	/app/data/pr_computation/ea/5ea0/5ea0.pr.out
profile	/app/data/saxs_computation/ea/5ea0/5ea0.dat

Structure of the antibody 7968 with human complement factor H-derived peptide

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

Complement factor H-related protein 2

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)