SAXSdb — 4p3b

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

Complement C5

Mus musculus

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 679–754	Fragment：UNP residues 679-754	FMT FORMIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.3；277 K；0.1 M Na acetate pH 4.3, 2.4 M Na Formate, 3 % D-glucose monohydrate	Resolution 2.10 Å R-free 0.224
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 679–754	Fragment：UNP residues 679-754	FMT FORMIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.3；277 K；0.1 M Na acetate pH 4.3, 2.4 M Na Formate, 3 % D-glucose monohydrate	Resolution 2.10 Å R-free 0.224
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 679–754	Fragment：UNP residues 679-754	FMT FORMIC ACID × 7	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.3；277 K；0.1 M Na acetate pH 4.3, 2.4 M Na Formate, 3 % D-glucose monohydrate	Resolution 2.10 Å R-free 0.224
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 679–754	Fragment：UNP residues 679-754	FMT FORMIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.3；277 K；0.1 M Na acetate pH 4.3, 2.4 M Na Formate, 3 % D-glucose monohydrate	Resolution 2.10 Å R-free 0.224
5	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 679–754 Chain C； UniProt 679–754	Fragment：UNP residues 679-754	FMT FORMIC ACID × 10	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.3；277 K；0.1 M Na acetate pH 4.3, 2.4 M Na Formate, 3 % D-glucose monohydrate	Resolution 2.10 Å R-free 0.224
6	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 679–754 Chain D； UniProt 679–754	Fragment：UNP residues 679-754	FMT FORMIC ACID × 5	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.3；277 K；0.1 M Na acetate pH 4.3, 2.4 M Na Formate, 3 % D-glucose monohydrate	Resolution 2.10 Å R-free 0.224

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 4P3B	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4P3A Crystal structure of the mouse C5a anaphylatoxin Deposited 2014-03-06	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 679–755（77 aa） Fragment：UNP residues 679-755	Not recorded	FMT FORMIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.7；277 K；0.1 M Na tri-citrate pH 3.7, 2.6 M Na formate, 0.5% (w/v) polyvinylpyrrolidone K15	Resolution 1.40 Å R-free 0.174
4P3A Crystal structure of the mouse C5a anaphylatoxin Deposited 2014-03-06	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 679–755（77 aa） Fragment：UNP residues 679-755	Not recorded	FMT FORMIC ACID × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.7；277 K；0.1 M Na tri-citrate pH 3.7, 2.6 M Na formate, 0.5% (w/v) polyvinylpyrrolidone K15	Resolution 1.40 Å R-free 0.174
4P3A Crystal structure of the mouse C5a anaphylatoxin Deposited 2014-03-06	Different construct Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 679–755（77 aa） Fragment：UNP residues 679-755	Not recorded	FMT FORMIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.7；277 K；0.1 M Na tri-citrate pH 3.7, 2.6 M Na formate, 0.5% (w/v) polyvinylpyrrolidone K15	Resolution 1.40 Å R-free 0.174
4P3A Crystal structure of the mouse C5a anaphylatoxin Deposited 2014-03-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 679–755（77 aa） Fragment：UNP residues 679-755	Not recorded	FMT FORMIC ACID × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.7；277 K；0.1 M Na tri-citrate pH 3.7, 2.6 M Na formate, 0.5% (w/v) polyvinylpyrrolidone K15	Resolution 1.40 Å R-free 0.174
4P3A Crystal structure of the mouse C5a anaphylatoxin Deposited 2014-03-06	Different construct Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 679–755（77 aa） Fragment：UNP residues 679-755 Chain B 679–755（77 aa） Fragment：UNP residues 679-755	Not recorded	FMT FORMIC ACID × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.7；277 K；0.1 M Na tri-citrate pH 3.7, 2.6 M Na formate, 0.5% (w/v) polyvinylpyrrolidone K15	Resolution 1.40 Å R-free 0.174
4P3A Crystal structure of the mouse C5a anaphylatoxin Deposited 2014-03-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 679–755（77 aa） Fragment：UNP residues 679-755 Chain D 679–755（77 aa） Fragment：UNP residues 679-755	Not recorded	FMT FORMIC ACID × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.7；277 K；0.1 M Na tri-citrate pH 3.7, 2.6 M Na formate, 0.5% (w/v) polyvinylpyrrolidone K15	Resolution 1.40 Å R-free 0.174
4WB2 Crystal structure of the mirror-image L-RNA/L-DNA aptamer NOX-D20 in complex with mouse C5a complement anaphylatoxin Deposited 2014-09-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 679–755（77 aa）	Not recorded	ACT ACETATE ION × 2 CA CALCIUM ION × 3 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；292 K；0.2 M NaCl, 0.1 M Na cacodylate pH 6.0, 8% (w/v) PEG 8000	Resolution 1.80 Å R-free 0.193
4WB2 Crystal structure of the mirror-image L-RNA/L-DNA aptamer NOX-D20 in complex with mouse C5a complement anaphylatoxin Deposited 2014-09-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 679–755（77 aa）	Not recorded	ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；292 K；0.2 M NaCl, 0.1 M Na cacodylate pH 6.0, 8% (w/v) PEG 8000	Resolution 1.80 Å R-free 0.193
4WB2 Crystal structure of the mirror-image L-RNA/L-DNA aptamer NOX-D20 in complex with mouse C5a complement anaphylatoxin Deposited 2014-09-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain C 679–755（77 aa）	Not recorded	ACT ACETATE ION × 2 CA CALCIUM ION × 3 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；292 K；0.2 M NaCl, 0.1 M Na cacodylate pH 6.0, 8% (w/v) PEG 8000	Resolution 1.80 Å R-free 0.193
4WB3 Crystal structure of the mirror-image L-RNA/L-DNA aptamer NOX-D20 in complex with mouse C5a-desArg complement anaphylatoxin Deposited 2014-09-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 679–754（76 aa）	Not recorded	CA CALCIUM ION × 3 ACT ACETATE ION × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；292 K；0.2 M ammonium acetate, 0.1 M Na acetate pH 4.0, 15% (w/v) PEG 4000	Resolution 2.00 Å R-free 0.199
4WB3 Crystal structure of the mirror-image L-RNA/L-DNA aptamer NOX-D20 in complex with mouse C5a-desArg complement anaphylatoxin Deposited 2014-09-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 679–754（76 aa）	Not recorded	ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；292 K；0.2 M ammonium acetate, 0.1 M Na acetate pH 4.0, 15% (w/v) PEG 4000	Resolution 2.00 Å R-free 0.199
4WB3 Crystal structure of the mirror-image L-RNA/L-DNA aptamer NOX-D20 in complex with mouse C5a-desArg complement anaphylatoxin Deposited 2014-09-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain C 679–754（76 aa）	Not recorded	CA CALCIUM ION × 3 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；292 K；0.2 M ammonium acetate, 0.1 M Na acetate pH 4.0, 15% (w/v) PEG 4000	Resolution 2.00 Å R-free 0.199
8JZP Structure of mouse C5a-human C5aR1-Go complex Deposited 2023-07-06	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain F 679–755（77 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.45 Å
9KWG Structure of mouse C5a bound mouse C5aR1 in complex with Go Deposited 2024-12-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain F 679–755（77 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.15 Å
9KWX Structure of mouse C5a-desArg bound mouse C5aR1 in complex with Go Deposited 2024-12-06	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain F 679–754（76 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.13 Å

6 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CO5_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–78； UniProt 679–754 Author chain B； PDBConstruct 3–78； UniProt 679–754 Author chain C； PDBConstruct 3–78； UniProt 679–754 Author chain D； PDBConstruct 3–78； UniProt 679–754

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	4p3b
Deposition date deposition_date	2014-03-06
Structure title title	Crystal structure of the mouse C5a-desArg anaphylatoxin
Keywords keywords	complement anaphylatoxin, C5a, four-helix bundle, GPCR agonist, 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	23.70 Å
Radius of gyration Rg (electron density) rg_electron	23.17 Å
Forward intensity I(0) i0	20199200.00
Molecular weight molecular_weight	32420.0 kDa
Excluded volume excluded_volume	40088 Å³
Envelope volume envelope_volume	52586 Å³
Hydration-shell volume shell_volume	20078 Å³
Envelope diameter envelope_diameter	74.6 Å
Shell Rg shell_rg	28.65 Å
Envelope Rg envelope_rg	23.16 Å
Shape Rg shape_rg	23.18 Å
Total Rg total_rg	23.88 Å
Total atoms total_atoms	2257
Residues n_residues	276
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	73.5 Å
Rg (real space) rg_real	23.67 Å
Rg uncertainty (real space) rg_real_error	0.40 Å
I(0) (real space) i0_real	2.0200e+07
I(0) uncertainty (real space) i0_real_error	2.4120e+05
Rg (reciprocal space) rg_reciprocal	23.68 Å
I(0) (reciprocal space) i0_reciprocal	20200000.0000
Solution quality estimate total_estimate	0.7164
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	32.2 Å
Skewness Skewness skewness	0.178
Kurtosis Kurtosis kurtosis	-0.660
Angular range angular_range	— – 0.3350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2701000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.968; Stabil: 1.000; Sysdev: 0.154; Positv: 1.000; Valcen: 0.951; Smooth: 0.992

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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	Complement C5
Molecular weight formula_weight	8890.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	2461

GANLHLLRQKIEEQAAKYKHSVPKKCCYDGARVNFYETCEERVARVTIGPLCIRAFNECCTIANKIRKESPHKPVQLG

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	15

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	204

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d4p3ba1
Class class	a — All alpha proteins
Fold Fold fold	a.50 — Anaphylotoxins (complement system)
Superfamily Superfamily superfamily	a.50.1 — Anaphylotoxins (complement system)
Family Family family	a.50.1.1 — Anaphylotoxins (complement system)

Domain ID domain_id	d4p3ba2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4p3bb1
Class class	a — All alpha proteins
Fold Fold fold	a.50 — Anaphylotoxins (complement system)
Superfamily Superfamily superfamily	a.50.1 — Anaphylotoxins (complement system)
Family Family family	a.50.1.1 — Anaphylotoxins (complement system)

Domain ID domain_id	d4p3bb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4p3bc1
Class class	a — All alpha proteins
Fold Fold fold	a.50 — Anaphylotoxins (complement system)
Superfamily Superfamily superfamily	a.50.1 — Anaphylotoxins (complement system)
Family Family family	a.50.1.1 — Anaphylotoxins (complement system)

Domain ID domain_id	d4p3bc2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4p3bd1
Class class	a — All alpha proteins
Fold Fold fold	a.50 — Anaphylotoxins (complement system)
Superfamily Superfamily superfamily	a.50.1 — Anaphylotoxins (complement system)
Family Family family	a.50.1.1 — Anaphylotoxins (complement system)

Domain ID domain_id	d4p3bd2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id	4p3bA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	91 — Influenza Virus Matrix Protein; Chain A, domain 1
Homologous superfamily homologous superfamily	20 — Anaphylotoxins (complement system)

Domain ID domain_id	4p3bB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	91 — Influenza Virus Matrix Protein; Chain A, domain 1
Homologous superfamily homologous superfamily	20 — Anaphylotoxins (complement system)

Domain ID domain_id	4p3bC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	91 — Influenza Virus Matrix Protein; Chain A, domain 1
Homologous superfamily homologous superfamily	20 — Anaphylotoxins (complement system)

Domain ID domain_id	4p3bD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	91 — Influenza Virus Matrix Protein; Chain A, domain 1
Homologous superfamily homologous superfamily	20 — Anaphylotoxins (complement system)

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8. Citations (1)

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Unit-cell length a length_a	55.210 Å
Unit-cell length b length_b	55.210 Å
Unit-cell length c length_c	117.430 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	16

Space group space_group	P 43
Space-group number int_tables_number	78
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	32.509 Å
R factor r_factor	0.1825
R_work r_work	0.1803
R_free r_free	0.2241

fit	/app/data/saxs_computation/p3/4p3b/4p3b.fit
pddf	/app/data/pr_computation/p3/4p3b/4p3b.pr.out
profile	/app/data/saxs_computation/p3/4p3b/4p3b.dat

Crystal structure of the mouse C5a-desArg anaphylatoxin

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

Complement C5

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