SAXSdb — 4yfs

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

Duffy receptor

Plasmodium vivax

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 198–521	Fragment：UNP RESIDUES 198-521	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M di-sodium tartrate, 20% PEG 3350, and microseeded into 0.2 M lithium chloride, 20% PEG 3350	Resolution 2.10 Å R-free 0.259

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 4YFS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3RRC Crystal Structure of Region II from Plasmodium vivax Duffy Binding Protein Deposited 2011-04-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 211–525（315 aa） Fragment：Region II (UNP residues 211-525) Chain B 211–525（315 aa） Fragment：Region II (UNP residues 211-525)	Not recorded	EDO 1,2-ETHANEDIOL × 11 PO4 PHOSPHATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；290 K；0.1 M ammonium phosphate, 23% polyethylene glycol 3350, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 1.95 Å R-free 0.241
4NUU Heterotrimer structure of Region II from Plasmodium vivax Duffy Binding Protein (PvDBP) bound to the ectodomain of the Duffy Antigen Receptor for Chemokines (DARC) Deposited 2013-12-04	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 211–525（315 aa） Fragment：unp residues 211-525	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；290 K；0.1 M HEPES and 20% (w/v) polyethylene glycol 6000, VAPOR DIFFUSION, HANGING DROP, temperature 290K, pH 7.4	Resolution 1.95 Å R-free 0.202
4NUU Heterotrimer structure of Region II from Plasmodium vivax Duffy Binding Protein (PvDBP) bound to the ectodomain of the Duffy Antigen Receptor for Chemokines (DARC) Deposited 2013-12-04	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 211–525（315 aa） Fragment：unp residues 211-525	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；290 K；0.1 M HEPES and 20% (w/v) polyethylene glycol 6000, VAPOR DIFFUSION, HANGING DROP, temperature 290K, pH 7.4	Resolution 1.95 Å R-free 0.202
4NUV Heterotetramer structure of Region II from Plasmodium vivax Duffy Binding Protein (PvDBP) bound to the ectodomain of the Duffy Antigen Receptor for Chemokines (DARC) Deposited 2013-12-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 211–525（315 aa） Fragment：unp residues 211-525 Chain B 211–525（315 aa） Fragment：unp residues 211-525	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；290 K；0.1 M HEPES and 20% (w/v) polyethylene glycol 6000, VAPOR DIFFUSION, HANGING DROP, temperature 290K, pH 7.4	Resolution 2.60 Å R-free 0.233
4NUV Heterotetramer structure of Region II from Plasmodium vivax Duffy Binding Protein (PvDBP) bound to the ectodomain of the Duffy Antigen Receptor for Chemokines (DARC) Deposited 2013-12-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 211–525（315 aa） Fragment：unp residues 211-525	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；290 K；0.1 M HEPES and 20% (w/v) polyethylene glycol 6000, VAPOR DIFFUSION, HANGING DROP, temperature 290K, pH 7.4	Resolution 2.60 Å R-free 0.233
4NUV Heterotetramer structure of Region II from Plasmodium vivax Duffy Binding Protein (PvDBP) bound to the ectodomain of the Duffy Antigen Receptor for Chemokines (DARC) Deposited 2013-12-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 211–525（315 aa） Fragment：unp residues 211-525	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；290 K；0.1 M HEPES and 20% (w/v) polyethylene glycol 6000, VAPOR DIFFUSION, HANGING DROP, temperature 290K, pH 7.4	Resolution 2.60 Å R-free 0.233
5F3J Crystal structure of DBP in complex with inhibitory monoclonal antibody 2D10 Deposited 2015-12-02	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 211–525（315 aa） Fragment：UNP residues 211-525	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；290 K；1% w/v tryptone, 50 mM HEPES sodium salt pH 7.0, 12% w/v PEG 3,350	Resolution 4.00 Å R-free 0.300
5F3J Crystal structure of DBP in complex with inhibitory monoclonal antibody 2D10 Deposited 2015-12-02	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 211–525（315 aa） Fragment：UNP residues 211-525	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；290 K；1% w/v tryptone, 50 mM HEPES sodium salt pH 7.0, 12% w/v PEG 3,350	Resolution 4.00 Å R-free 0.300
6R2S The structure of Plasmodium vivax Duffy binding protein (PvDBP) bound to human antibody DB9 Deposited 2019-03-18	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 211–508（298 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；45 % v/v polypropylene glycol 400, 10% v/v ethanol	Resolution 3.04 Å R-free 0.238
9EZE Structure of subdomain 3 of the Plasmodium vivx Duffy binding protein (PvDBP) bound to human antibody DB9 Deposited 2024-04-11	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 211–508（298 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M ammonium acetate, 0.1M sodium acetate pH 4.0, 15% PEG 4000	Resolution 1.55 Å R-free 0.223
9EZE Structure of subdomain 3 of the Plasmodium vivx Duffy binding protein (PvDBP) bound to human antibody DB9 Deposited 2024-04-11	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 211–508（298 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M ammonium acetate, 0.1M sodium acetate pH 4.0, 15% PEG 4000	Resolution 1.55 Å R-free 0.223

6 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PVDR_PLAVS
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–326； UniProt 198–521

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	4yfs
Deposition date deposition_date	2015-02-25
Structure title title	Structure of the synthetic Duffy Binding Protein (DBP) antigen DEKnull relevant for malaria vaccine design
Keywords keywords	Duffy binding like domain, invasion, malaria, vaccine, Erythrocyte binding protein; Erythrocyte binding protein
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	22.30 Å
Radius of gyration Rg (electron density) rg_electron	21.84 Å
Forward intensity I(0) i0	19828500.00
Molecular weight molecular_weight	33749.0 kDa
Excluded volume excluded_volume	42303 Å³
Envelope volume envelope_volume	50754 Å³
Hydration-shell volume shell_volume	20538 Å³
Envelope diameter envelope_diameter	87.7 Å
Shell Rg shell_rg	27.35 Å
Envelope Rg envelope_rg	22.50 Å
Shape Rg shape_rg	21.78 Å
Total Rg total_rg	22.77 Å
Total atoms total_atoms	4733
Residues n_residues	285
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	85.9 Å
Rg (real space) rg_real	22.45 Å
Rg uncertainty (real space) rg_real_error	0.90 Å
I(0) (real space) i0_real	1.9830e+07
I(0) uncertainty (real space) i0_real_error	2.9400e+05
Rg (reciprocal space) rg_reciprocal	22.41 Å
I(0) (reciprocal space) i0_reciprocal	19830000.0000
Solution quality estimate total_estimate	0.7836
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.4 Å
Skewness Skewness skewness	0.620
Kurtosis Kurtosis kurtosis	0.244
Angular range angular_range	— – 0.3550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6367000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.503; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.725; Smooth: 0.949

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4yfsa_
Class class	a — All alpha proteins
Fold Fold fold	a.264 — Duffy binding domain-like
Superfamily Superfamily superfamily	a.264.1 — Duffy binding domain-like
Family Family family	a.264.1.1 — Duffy binding domain

CATH v4.4 (2 domains)

Domain ID domain_id	4yfsA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1310 — 5 helical Cullin repeat like
Homologous superfamily homologous superfamily	20 — Duffy-antigen binding domain

Domain ID domain_id	4yfsA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	830 —

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8. Citations (1)

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Unit-cell length a length_a	55.630 Å
Unit-cell length b length_b	37.350 Å
Unit-cell length c length_c	78.200 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	108.77 °
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	2.100 Å
Low-resolution limit resolution_low	26.536 Å
R factor r_factor	0.2220
R_work r_work	0.2177
R_free r_free	0.2588

Description description	Duffy receptor
Molecular weight formula_weight	38257.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4907

Structure of the synthetic Duffy Binding Protein (DBP) antigen DEKnull relevant for malaria vaccine design

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

Duffy receptor

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Plasmodium vivax
NCBI Class编号 ncbi_taxonomy_id	126793
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	128

fit	/app/data/saxs_computation/yf/4yfs/4yfs.fit
pddf	/app/data/pr_computation/yf/4yfs/4yfs.pr.out
profile	/app/data/saxs_computation/yf/4yfs/4yfs.dat