9LU3 | pdb_00009lu3

LN1F9 Fab bound to Nipah Virus attachment (G) glycoprotein head domain

PDB DOI: https://doi.org/10.2210/pdb9LU3/pdb

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Henipavirus nipahense, Mus musculus
Expression System: Homo, Homo sapiens
Mutation(s): No

Deposited: 2025-02-07 Released: 2025-11-26
Deposition Author(s): Deng, Z., Kuang, W.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.269 (Depositor), 0.268 (DCC)
R-Value Work:
0.219 (Depositor), 0.221 (DCC)
R-Value Observed:
0.222 (Depositor)

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

Ligand Structure Quality Assessment

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

Literature

Antigenic landscape of Nipah virus attachment glycoprotein analysis reveals a protective immunodominant epitope across species

Zhou, D., Wang, Y., Yao, Y., Kuang, W., Cheng, R., Zhang, G., Liu, H., Li, X., Chiu, S., Deng, Z., Zhao, H.

(2025) NPJ Vaccines

Macromolecule Content

Total Structure Weight: 198.64 kDa
Atom Count: 13,333
Modeled Residue Count: 1,703
Deposited Residue Count: 1,778
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoprotein G	A, D [auth B]	441	Henipavirus nipahense	Mutation(s): 0
UniProt
Find proteins for Q9IH62 (Nipah virus) Explore Q9IH62 Go to UniProtKB: Q9IH62
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9IH62
Glycosylation
Glycosylation Sites: 5	Glycosylation Focus chain A Focus chain D [auth B]
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
mAb LN1F9 Fab heavy chain	B [auth H], E [auth D]	234	Mus musculus	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
mAb LN1F9 Fab light chain	C [auth L], F [auth E]	214	Mus musculus	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
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth A] G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]