9DST | pdb_00009dst

Crystal structure of Fab MS-1805 in complex with N-terminal junction peptide from circumsporozoite protein

PDB DOI: https://doi.org/10.2210/pdb9DST/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens, Plasmodium falciparum 3D7
Expression System: Cricetulus griseus, synthetic construct
Mutation(s): No

Deposited: 2024-09-28 Released: 2025-10-01
Deposition Author(s): Jain, M., Wilson, I.A.
Funding Organization(s): Bill & Melinda Gates Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free:
0.228 (Depositor), 0.228 (DCC)
R-Value Work:
0.197 (Depositor), 0.197 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of Fab MS-1805 in complex with N-terminal junction peptide from circumsporozoite protein

Jain, M., Wilson, I.A.

To be published.

Macromolecule Content

Total Structure Weight: 49.76 kDa
Atom Count: 3,545
Modeled Residue Count: 440
Deposited Residue Count: 458
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Light Chain of Fab MS-1805	A [auth D]	215	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: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Circumsporozoite protein	B [auth A]	16	Plasmodium falciparum 3D7	Mutation(s): 0 Gene Names: CSP, PF3D7_0304600
UniProt
Find proteins for Q7K740 (Plasmodium falciparum (isolate 3D7)) Explore Q7K740 Go to UniProtKB: Q7K740
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7K740
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of Fab MS-1805	C	227	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain D [auth C] MOL2 format, chain D [auth C] mmCIF format, chain D [auth C]	D [auth C]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain D [auth C] Interactions & Density Focus chain D [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free: 0.228 (Depositor), 0.228 (DCC)
R-Value Work: 0.197 (Depositor), 0.197 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.325	α = 90
b = 76.744	β = 88.38
c = 74.453	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-01

Deposition Author(s):

Funding Organization	Location	Grant Number
Bill & Melinda Gates Foundation	United States	INV-004923
Bill & Melinda Gates Foundation	United States	INV-056202

Revision History (Full details and data files)

Version 1.0: 2025-10-01
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.