8PWX

PfRH5 bound to monoclonal antibody R5.008

PDB DOI: https://doi.org/10.2210/pdb8PWX/pdb

Classification: CELL ADHESION
Organism(s): Homo sapiens, Plasmodium falciparum 3D7
Expression System: Homo sapiens, Drosophila melanogaster
Mutation(s): No

Deposited: 2023-07-21 Released: 2024-06-05
Deposition Author(s): Farrell, B., Higgins, M.K.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.293
R-Value Work: 0.240
R-Value Observed: 0.243

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

PfRH5 bound to monoclonal antibody R5.008

Farrell, B., Higgins, M.K.

To be published.

Macromolecule Content

Total Structure Weight: 70.79 kDa
Atom Count: 4,241
Modelled Residue Count: 524
Deposited Residue Count: 622
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv fragment for antibody R5.008	A	284	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Reticulocyte-binding protein homolog 5	B	338	Plasmodium falciparum 3D7	Mutation(s): 0 Gene Names: RH5, PFD1145c, PF3D7_0424100
UniProt
Find proteins for Q8IFM5 (Plasmodium falciparum (isolate 3D7)) Explore Q8IFM5 Go to UniProtKB: Q8IFM5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8IFM5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.293
R-Value Work: 0.240
R-Value Observed: 0.243
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.99	α = 90
b = 114.99	β = 90
c = 147.494	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
PHENIX	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-06-05

Deposition Author(s):

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	220797/Z/20/Z

Revision History (Full details and data files)

Version 1.0: 2024-06-05
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.