SAXSdb — 4wb3

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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–DNA Monomer Protein × 1 DNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts	Chain A； UniProt 679–754	Not recorded	mixed L-RNA/L-DNA aptamer NOX-D20 (40-MER) × 1 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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 679–754	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
3	Protein–DNA Monomer Protein × 1 DNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts	Chain C； UniProt 679–754	Not recorded	mixed L-RNA/L-DNA aptamer NOX-D20 (40-MER) × 1 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

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 4WB3	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 ligand/ion 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 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） 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 ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state 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
4P3B Crystal structure of the mouse C5a-desArg anaphylatoxin Deposited 2014-03-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 679–754（76 aa） Fragment：UNP residues 679-754	Not recorded	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
4P3B Crystal structure of the mouse C5a-desArg anaphylatoxin Deposited 2014-03-06	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） Fragment：UNP residues 679-754	Not recorded	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
4P3B Crystal structure of the mouse C5a-desArg anaphylatoxin Deposited 2014-03-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 679–754（76 aa） Fragment：UNP residues 679-754	Not recorded	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
4P3B Crystal structure of the mouse C5a-desArg 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 679–754（76 aa） Fragment：UNP residues 679-754	Not recorded	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
4P3B Crystal structure of the mouse C5a-desArg anaphylatoxin Deposited 2014-03-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 679–754（76 aa） Fragment：UNP residues 679-754 Chain C 679–754（76 aa） Fragment：UNP residues 679-754	Not recorded	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
4P3B Crystal structure of the mouse C5a-desArg anaphylatoxin Deposited 2014-03-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 679–754（76 aa） Fragment：UNP residues 679-754 Chain D 679–754（76 aa） Fragment：UNP residues 679-754	Not recorded	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
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 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 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 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
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 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 18 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

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	4wb3
Deposition date deposition_date	2014-09-02
Structure title title	Crystal structure of the mirror-image L-RNA/L-DNA aptamer NOX-D20 in complex with mouse C5a-desArg complement anaphylatoxin
Keywords keywords	protein-RNA complex, mirror-image aptamer, G-quadruplex, complement anaphylatoxin, DNA-RNA hybrid; DNA-RNA HYBRID
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	28.49 Å
Radius of gyration Rg (electron density) rg_electron	28.95 Å
Forward intensity I(0) i0	115266000.00
Molecular weight molecular_weight	47395.0 kDa
Excluded volume excluded_volume	40379 Å³
Envelope volume envelope_volume	77893 Å³
Hydration-shell volume shell_volume	23620 Å³
Envelope diameter envelope_diameter	103.6 Å
Shell Rg shell_rg	34.46 Å
Envelope Rg envelope_rg	29.06 Å
Shape Rg shape_rg	29.11 Å
Total Rg total_rg	29.07 Å
Total atoms total_atoms	3389
Residues n_residues	205
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	99.0 Å
Rg (real space) rg_real	28.73 Å
Rg uncertainty (real space) rg_real_error	0.82 Å
I(0) (real space) i0_real	1.1530e+08
I(0) uncertainty (real space) i0_real_error	1.9920e+06
Rg (reciprocal space) rg_reciprocal	28.67 Å
I(0) (reciprocal space) i0_reciprocal	115300000.0000
Solution quality estimate total_estimate	0.8397
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.8 Å
Skewness Skewness skewness	0.417
Kurtosis Kurtosis kurtosis	-0.497
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4497000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.768; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.625; Smooth: 0.984

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	3779

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 polymer

Description description	mixed L-RNA/L-DNA aptamer NOX-D20 (40-MER)
Molecular weight formula_weight	12956.7 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide/polyribonucleotide hybrid
Chain IDs strand_id	D,E

GCGXUGXGGUGGUGAXGGGUUGUUGGGXGXCGXCGCXCGC

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	373

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	4wb3A00
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	4wb3B00
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	4wb3C00
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	45.840 Å
Unit-cell length b length_b	282.630 Å
Unit-cell length c length_c	45.760 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	12

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	32.852 Å
R factor r_factor	0.1645
R_work r_work	0.1626
R_free r_free	0.1994

fit	/app/data/saxs_computation/wb/4wb3/4wb3.fit
pddf	/app/data/pr_computation/wb/4wb3/4wb3.pr.out
profile	/app/data/saxs_computation/wb/4wb3/4wb3.dat

Crystal structure of the mirror-image L-RNA/L-DNA aptamer NOX-D20 in complex with mouse C5a-desArg complement 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

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)