SAXSdb — 5f3j

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

Duffy receptor

Plasmodium vivax (strain Salvador I)

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 211–525	Fragment：UNP residues 211-525	Antibody 2D10 single chain variable fragment × 1	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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 211–525	Fragment：UNP residues 211-525	Antibody 2D10 single chain variable fragment × 1	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

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 5F3J	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 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 oligomeric state 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 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 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
4YFS Structure of the synthetic Duffy Binding Protein (DBP) antigen DEKnull relevant for malaria vaccine design Deposited 2015-02-25	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 198–521（324 aa） Fragment：UNP RESIDUES 198-521	Not recorded	No recorded non-water small molecule	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
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 10 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 3–317； UniProt 211–525 Author chain B； PDBConstruct 3–317； UniProt 211–525

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	5f3j
Deposition date deposition_date	2015-12-02
Structure title title	Crystal structure of DBP in complex with inhibitory monoclonal antibody 2D10
Keywords keywords	;Plasmodium, vivax, duffy binding protein, DBP, antibody, malaria, scfv, neutralizing, interaction, immune, blocking, invasion, vaccine, therapeutic, 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	54.28 Å
Radius of gyration Rg (electron density) rg_electron	55.27 Å
Forward intensity I(0) i0	178936000.00
Molecular weight molecular_weight	109770.0 kDa
Excluded volume excluded_volume	137170 Å³
Envelope volume envelope_volume	220200 Å³
Hydration-shell volume shell_volume	37463 Å³
Envelope diameter envelope_diameter	174.2 Å
Shell Rg shell_rg	48.09 Å
Envelope Rg envelope_rg	53.37 Å
Shape Rg shape_rg	55.23 Å
Total Rg total_rg	55.11 Å
Total atoms total_atoms	7719
Residues n_residues	956
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	166.7 Å
Rg (real space) rg_real	55.00 Å
Rg uncertainty (real space) rg_real_error	1.41 Å
I(0) (real space) i0_real	1.7890e+08
I(0) uncertainty (real space) i0_real_error	3.7920e+06
Rg (reciprocal space) rg_reciprocal	53.62 Å
I(0) (reciprocal space) i0_reciprocal	178600000.0000
Solution quality estimate total_estimate	0.6637
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	28.8 Å
Skewness Skewness skewness	0.422
Kurtosis Kurtosis kurtosis	-0.960
Angular range angular_range	— – 0.1450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4664000.0000
Real-space data points n_real_points	30
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.468; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.221; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Duffy receptor
Molecular weight formula_weight	37610.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7719

ASNTVMKNCNYKRKRRERDWDCNTKKDVCIPDRRYQLCMKELTNLVNNTDTNFHRDITFRKLYLKRKLIYDAAVEGDLLLKLNNYRYNKDFCKDIRWSLGDFGDIIMGTDMEGIGYSKVVENNLRSIFGTDEKAQQRRKQWWNESKAQIWTAMMYSVKKRLKGNFIWICKLNVAVNIEPQIYRWIREWGRDYVSELPTEVQKLKEKCDGKINYTDKKVCKVPPCQNACKSYDQWITRKKNQWDVLSNKFISVKNAEKVQTAGIVTPYDILKQELDEFNEVAFENEINKRDGAYIELCVCSVEEAKKNTQEVVTNVDN

来源 Source

来源生物 organism	Plasmodium vivax (strain Salvador I)
NCBI Class编号 ncbi_taxonomy_id	126793
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Antibody 2D10 single chain variable fragment
Molecular weight formula_weight	32227.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

MGILPSPGMPALLSLVSLLSVLLMGCVAETGLAAQPAMADIVITQDELSNPVTSGESVSISCRSSKSLLYQDGKTYLNWFLQRPGQSPQLLIYLMSTRASGVSDRFSGSGSGTDFTLEISRVEAEDVGVYYCQQLVEYPLTFGAGTKLELKRADGGGGSGGGGSGGGGSQVQLQQSGPELVKPGASVKISCKASGYAFISSWMNWVKQRPGKGLEWIGRIYPGDGDTHYNGKFKGKATLTADKSSSTAYMQLSSLTSEDSAVYFCAREETAQTGGFDYWGQGTTLTVSSEASGADHGTKHHHHHH

来源 Source

来源生物 organism	Mus musculus
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Homo sapiens

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7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	5f3jA01
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	5f3jA02
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 —

Domain ID domain_id	5f3jB01
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	5f3jB02
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 —

Domain ID domain_id	5f3jC01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5f3jD01
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	84.940 Å
Unit-cell length b length_b	63.940 Å
Unit-cell length c length_c	108.880 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.09 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	4.001 Å
Low-resolution limit resolution_low	19.944 Å
R factor r_factor	0.2686
R_work r_work	0.2669
R_free r_free	0.2997

fit	/app/data/saxs_computation/f3/5f3j/5f3j.fit
pddf	/app/data/pr_computation/f3/5f3j/5f3j.pr.out
profile	/app/data/saxs_computation/f3/5f3j/5f3j.dat

Crystal structure of DBP in complex with inhibitory monoclonal antibody 2D10

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 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)