← Back to search
9eze

Structure of subdomain 3 of the Plasmodium vivx Duffy binding protein (PvDBP) bound to human antibody DB9

Method: X-RAY DIFFRACTION Dmax: 128.8 Å Quality: REASONABLE
▼

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

Duffy receptor

Plasmodium vivax Sal-1

UniProt P22290

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 211–508 Not recorded Antibody DB9 heavy chain × 1 Antibody DB9 light chain × 1 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
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain D； UniProt 211–508 Not recorded Antibody DB9 heavy chain × 1 Antibody DB9 light chain × 1 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

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 9EZE 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 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 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
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
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 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

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 3–300； UniProt 211–508 Author chain D； PDBConstruct 3–300； UniProt 211–508

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.

SAXS scattering curve SAXS Profile

SAXS profile for 9eze

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9eze
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id9eze
Deposition date deposition_date2024-04-11
最后修订 last_revision2025-10-29
Structure title titleStructure of subdomain 3 of the Plasmodium vivx Duffy binding protein (PvDBP) bound to human antibody DB9
Keywords keywordsPvDBP, Plasmodium vivax, erythrocyte invasion, monoclonal antibody, rational vaccine design, CELL ADHESION; CELL ADHESION
Experimental Method methodX-RAY DIFFRACTION
▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier36.90 Å
Radius of gyration Rg (electron density) rg_electron36.61 Å
Forward intensity I(0) i0228855000.00
Molecular weight molecular_weight121010.0 kDa
Excluded volume excluded_volume151180 ų
Envelope volume envelope_volume207490 ų
Hydration-shell volume shell_volume48838 ų
Envelope diameter envelope_diameter131.3 Å
Shell Rg shell_rg41.27 Å
Envelope Rg envelope_rg36.13 Å
Shape Rg shape_rg36.58 Å
Total Rg total_rg37.05 Å
Total atoms total_atoms8524
Residues n_residues1107
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax128.8 Å
Rg (real space) rg_real37.00 Å
Rg uncertainty (real space) rg_real_error1.34 Å
I(0) (real space) i0_real2.2890e+08
I(0) uncertainty (real space) i0_real_error3.9470e+06
Rg (reciprocal space) rg_reciprocal36.94 Å
I(0) (reciprocal space) i0_reciprocal228800000.0000
Solution quality estimate total_estimate0.6429
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary41.9 Å
Skewness Skewness skewness0.444
Kurtosis Kurtosis kurtosis-0.150
Angular range angular_range— – 0.2150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha23580000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.791; Stabil: 1.000; Sysdev: 0.048; Positv: 1.000; Valcen: 0.943; Smooth: 0.893
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

▶

8. Citations (1)

▶

9. Files and Curves (10)