9RA5 | pdb_00009ra5

Respiratory syncytial virus fusion protein N-terminal heptad repeat domain in complex with Double stapled peptide 3/4i

PDB DOI: https://doi.org/10.2210/pdb9RA5/pdb

Classification: ANTIVIRAL PROTEIN
Organism(s): Human respiratory syncytial virus A, human respiratory syncytial virus
Mutation(s): Yes

Deposited: 2025-05-20 Released: 2026-06-03
Deposition Author(s): Duquerroy, S., Nyanguile, O., Gsponer, N., Nicolet, N., Marti, R.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free:
0.207 (Depositor), 0.201 (DCC)
R-Value Work:
0.193 (Depositor), 0.183 (DCC)
R-Value Observed:
0.194 (Depositor)

Starting Model: experimental
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Literature

Double stapled peptide scan yields 3/4i, a potent fusion inhibitor of Respiratory Syncytial Virus

Gsponer, N., Nicolet, N., Marti, R., Duquerroy, S., Nyanguile, O.

To be published.

Macromolecule Content

Total Structure Weight: 8.04 kDa
Atom Count: 566
Modeled Residue Count: 68
Deposited Residue Count: 75
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion glycoprotein F1	A	53	Human respiratory syncytial virus A	Mutation(s): 2
UniProt
Find proteins for P03420 (Human respiratory syncytial virus A (strain A2)) Explore P03420 Go to UniProtKB: P03420
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03420
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Double stapled peptide 3/4i	B [auth D]	22	human respiratory syncytial virus	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL (Subject of Investigation/LOI) 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] Interactions & Density Focus chain C [auth A]
K (Subject of Investigation/LOI) Query on K Download:Ideal Coordinates CCD File SDF format, chain D MOL2 format, chain D mmCIF format, chain D	D	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain D Interactions & Density Focus chain D

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
2JN Query on 2JN	B [auth D]	D-PEPTIDE LINKING	C₇ H₁₅ N O₂		--
MK8 Query on MK8	B [auth D]	L-PEPTIDE LINKING	C₇ H₁₅ N O₂		LEU

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free: 0.207 (Depositor), 0.201 (DCC)
R-Value Work: 0.193 (Depositor), 0.183 (DCC)
R-Value Observed: 0.194 (Depositor)

Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.32	α = 90
b = 78.32	β = 90
c = 78.32	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
autoPROC	data processing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-06-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	Switzerland	HES-SO 78166/IA-INTERDISC17-2

Revision History (Full details and data files)

Version 1.0: 2026-06-03
Type: Initial release

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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.