SAXSdb — 6rv6

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

Properdin

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 4 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 28–191 Chain B； UniProt 256–469	Not recorded	beta-D-glucopyranose-(1-3)-alpha-L-fucopyranose × 3 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MAN alpha-D-mannopyranose × 12	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4；292 K；1.0 M lithium sulfate, 0.1 M sodium acetate pH 4.0, 0.1 M barium chloride	Resolution 3.51 Å R-free 0.283

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 6RV6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1W0R Solution structure of dimeric form of properdin by X-ray solution scattering and analytical ultracentrifugation Deposited 2004-06-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–469（442 aa） Fragment：RESIDUES 28-469	Not recorded	No recorded non-water small molecule	SOLUTION SCATTERING mmCIF provides none of the parsed conditions	Resolution not provided
1W0R Solution structure of dimeric form of properdin by X-ray solution scattering and analytical ultracentrifugation Deposited 2004-06-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 28–469（442 aa） Fragment：RESIDUES 28-469	Not recorded	No recorded non-water small molecule	SOLUTION SCATTERING mmCIF provides none of the parsed conditions	Resolution not provided
1W0S Solution structure of trimeric form of properdin by X-ray solution scattering and analytical ultracentrifugation Deposited 2004-06-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–469（442 aa） Fragment：RESIDUES 28-469	Not recorded	No recorded non-water small molecule	SOLUTION SCATTERING mmCIF provides none of the parsed conditions	Resolution not provided
1W0S Solution structure of trimeric form of properdin by X-ray solution scattering and analytical ultracentrifugation Deposited 2004-06-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 28–469（442 aa） Fragment：RESIDUES 28-469	Not recorded	No recorded non-water small molecule	SOLUTION SCATTERING mmCIF provides none of the parsed conditions	Resolution not provided
1W0S Solution structure of trimeric form of properdin by X-ray solution scattering and analytical ultracentrifugation Deposited 2004-06-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 28–469（442 aa） Fragment：RESIDUES 28-469	Not recorded	No recorded non-water small molecule	SOLUTION SCATTERING mmCIF provides none of the parsed conditions	Resolution not provided
6RUR Structure of the SCIN stabilized C3bBb convertase bound to properdin Deposited 2019-05-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain U 28–255（228 aa） Chain V 256–469（214 aa） Chain X 28–255（228 aa） Chain Y 256–469（214 aa）	Mutation：TSR2 and TSR3 are not modelled Mutation：TSR2 and TSR3 are not modelled	MAN alpha-D-mannopyranose × 18 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；50 mM MgAcetate 50 mM Mes 6.5 5 % w/v PEG 10K	Resolution 6.00 Å R-free 0.272
6RUS Structure of a functional properdin monomer Deposited 2019-05-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–255（228 aa）	Not recorded	MAN alpha-D-mannopyranose × 8 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；1.1 M ammonium sulfate, 0.1 M sodium acetate pH 6.0, 1.2%(w/v) myo-inositol	Resolution 2.80 Å R-free 0.274
6RUS Structure of a functional properdin monomer Deposited 2019-05-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 256–469（214 aa）	Not recorded	MAN alpha-D-mannopyranose × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；1.1 M ammonium sulfate, 0.1 M sodium acetate pH 6.0, 1.2%(w/v) myo-inositol	Resolution 2.80 Å R-free 0.274
6RUV Structure of the SCIN stabilized C3bBb convertase bound to Properdin and a the non-inhibitory nanobody hFPNb1 Deposited 2019-05-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain U 28–191（164 aa） Chain V 256–469（214 aa） Chain X 28–191（164 aa） Chain Y 256–469（214 aa）	Not recorded	MAN alpha-D-mannopyranose × 21 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.8；277 K；100 mM NaCl, 5 % (w/v) PEG4000, 10 mM MgCl2, 100 mM Sodium Cacodylate trihydrate pH 5.8.	Resolution 6.15 Å R-free 0.271
6S08 Crystal Structure of Properdin (TSR domains N1 & 456) Deposited 2019-06-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 256–469（214 aa） Chain B 26–132（107 aa）	Not recorded	MAN alpha-D-mannopyranose × 8 PGE TRIETHYLENE GLYCOL × 1 NA SODIUM ION × 1 FUC alpha-L-fucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Potassium Sulphate, PEG 3350	Resolution 2.03 Å R-free 0.248
6S0A Crystal Structure of Properdin (TSR domains N12 & 456) Deposited 2019-06-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 256–469（214 aa） Chain B 26–191（166 aa）	Not recorded	MAN alpha-D-mannopyranose × 10 FUC alpha-L-fucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；Sodium Citrate, PEG 3000	Resolution 2.52 Å R-free 0.267
6S0B Crystal Structure of Properdin in complex with the CTC domain of C3/C3b Deposited 2019-06-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 256–469（214 aa） Chain B 26–132（107 aa）	Not recorded	MAN alpha-D-mannopyranose × 8 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；Tacsimate, PEG 3350	Resolution 2.31 Å R-free 0.277
6SEJ Structure of a functional monomeric properdin lacking TSR3 Deposited 2019-07-30	Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 28–191（164 aa） Chain B 256–469（214 aa）	Not recorded	MAN alpha-D-mannopyranose × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；292 K；1.0 M lithium sulfate, 0.1 M sodium acetate pH 4.0, 0.1 M barium chloride	Resolution 3.50 Å R-free 0.266
7B26 CirpA1 in complex with pseudo-monomeric Properdin lacking TSR2-3 Deposited 2020-11-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–134（134 aa） Chain B 256–469（214 aa）	Not recorded	MAN alpha-D-mannopyranose × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.15 M Potassium thiocyanate, 0.1 M Tris, pH 7.5, 18 % w/v PEG 5000 MME	Resolution 3.40 Å R-free 0.274
7NOZ Structure of the nanobody stablized properdin bound alternative pathway proconvertase C3b:FB:FP Deposited 2021-02-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 28–190（163 aa） Chain D 255–461（207 aa）	Not recorded	MAN alpha-D-mannopyranose × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.05 M Na-acetate pH 5.3, 0.1 M Mg-formate,7% PEG5000 MME	Resolution 3.90 Å R-free 0.265
8Q6R Structure of complement FP in complex with the TPP-3077 VHH Deposited 2023-08-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 28–135（108 aa） Chain D 256–469（214 aa）	Not recorded	GCH GLYCOCHOLIC ACID × 2 MAN alpha-D-mannopyranose × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；292 K；95% Morpheus Screen III, condition G1	Resolution 1.90 Å R-free 0.238
8Q6R Structure of complement FP in complex with the TPP-3077 VHH Deposited 2023-08-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 28–135（108 aa） Chain F 256–469（214 aa）	Not recorded	MAN alpha-D-mannopyranose × 10 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；292 K；95% Morpheus Screen III, condition G1	Resolution 1.90 Å R-free 0.238
9U62 AP pathways C3 convertase C3bBbP and C3 complex Deposited 2025-03-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain P 1–453（453 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 NI NICKEL (II) ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å

13 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PROP_HUMAN
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–164； UniProt 28–191 Author chain B； PDBConstruct 2–215； UniProt 256–469

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	6rv6
Deposition date deposition_date	2019-05-31
Structure title title	Structure of properdin lacking TSR3 based on anomalous data
Keywords keywords	innate immunity, complement, protease, regulator, 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	37.06 Å
Radius of gyration Rg (electron density) rg_electron	37.39 Å
Forward intensity I(0) i0	40434400.00
Molecular weight molecular_weight	45931.0 kDa
Excluded volume excluded_volume	55807 Å³
Envelope volume envelope_volume	93786 Å³
Hydration-shell volume shell_volume	24508 Å³
Envelope diameter envelope_diameter	134.1 Å
Shell Rg shell_rg	36.55 Å
Envelope Rg envelope_rg	37.43 Å
Shape Rg shape_rg	37.37 Å
Total Rg total_rg	37.39 Å
Total atoms total_atoms	3191
Residues n_residues	385
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	126.0 Å
Rg (real space) rg_real	37.44 Å
Rg uncertainty (real space) rg_real_error	1.60 Å
I(0) (real space) i0_real	4.0430e+07
I(0) uncertainty (real space) i0_real_error	6.8510e+05
Rg (reciprocal space) rg_reciprocal	37.21 Å
I(0) (reciprocal space) i0_reciprocal	40430000.0000
Solution quality estimate total_estimate	0.8383
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	41.0 Å
Skewness Skewness skewness	0.398
Kurtosis Kurtosis kurtosis	-0.596
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1350000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.813; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.636; Smooth: 0.818

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Properdin
Molecular weight formula_weight	18636.9 kDa
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	3191

DPVLCFTQYEESSGKCKGLLGGGVSVEDCCLNTAFAYQKRSGGLCQPCRSPRWSLWSTWAPCSVTCSEGSQLRYRRCVGWNGQCSGKVAPGTLEWQLQACEDQQCCPEMGGWSGWGPWEPCSVTCSKGTRTRRRACNHPAPKCGGHCPGQAQESEACDTQQVCPENLYFQ

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 polymer

Description description	Properdin
Molecular weight formula_weight	24724.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GVAGGWGPWGPVSPCPVTCGLGQTMEQRTCNHPVPQHGGPFCAGDATRTHICNTAVPCPVDGEWDSWGEWSPCIRRNMKSISCQEIPGQQSRGRTCRGRKFDGHRCAGQQQDIRHCYSIQHCPLKGSWSEWSTWGLCMPPCGPNPTRARQRLCTPLLPKYPPTVSMVEGQGEKNVTFWGRPLPRCEELQGQKLVVEEKRPCLHVPACKDPEEEELENLYFQ

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 3 Entity 3 branched

Description description	beta-D-glucopyranose-(1-3)-alpha-L-fucopyranose
Molecular weight formula_weight	326.3 kDa
Source method src_method	man
Copy count entity_count	3

Entity 4 Entity 4 branched

Description description	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	570.5 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	alpha-D-mannopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	man
Copy count entity_count	12

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8. Citations (3)

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Unit-cell length a length_a	219.790 Å
Unit-cell length b length_b	219.790 Å
Unit-cell length c length_c	47.440 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	I 41
Space-group number int_tables_number	80
Crystal system crystal_system	—

Resolution resolution	3.507 Å
Low-resolution limit resolution_low	77.707 Å
R factor r_factor	0.2649
R_work r_work	0.2641
R_free r_free	0.2835

fit	/app/data/saxs_computation/rv/6rv6/6rv6.fit
pddf	/app/data/pr_computation/rv/6rv6/6rv6.pr.out
profile	/app/data/saxs_computation/rv/6rv6/6rv6.dat

Structure of properdin lacking TSR3 based on anomalous data

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

Properdin

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

8. Citations (3)

9. Files and Curves (10)

Files (7)

Curves (3)