9EZE | pdb_00009eze

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

PDB DOI: https://doi.org/10.2210/pdb9EZE/pdb

Classification: CELL ADHESION
Organism(s): Plasmodium vivax Sal-1, Homo sapiens
Expression System: Escherichia coli, Homo sapiens
Mutation(s): No

Deposited: 2024-04-11 Released: 2025-10-29
Deposition Author(s): Barber, N.M., Higgins, M.K.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.223 (Depositor), 0.195 (DCC)
R-Value Work:
0.204 (Depositor), 0.199 (DCC)
R-Value Observed:
0.205 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Subdomain 3 of the Plasmodium vivax Duffy binding protein as a vaccine candidate

Barber, N.M., Higgins, M.K.

To be published.

Macromolecule Content

Total Structure Weight: 181.13 kDa
Atom Count: 9,514
Modeled Residue Count: 1,107
Deposited Residue Count: 1,622
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Duffy receptor	A, D	300	Plasmodium vivax Sal-1	Mutation(s): 0 Gene Names: PVDR
UniProt
Find proteins for P22290 (Plasmodium vivax (strain Salvador I)) Explore P22290 Go to UniProtKB: P22290
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P22290
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody DB9 heavy chain	B, E	278	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody DB9 light chain	C, F	233	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.223 (Depositor), 0.195 (DCC)
R-Value Work: 0.204 (Depositor), 0.199 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.427	α = 90
b = 126.191	β = 90
c = 129.863	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2025-10-29

Deposition Author(s):

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	--

Revision History (Full details and data files)

Version 1.0: 2025-10-29
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.