9SL0 | pdb_00009sl0

Crystal structure of HLA-A0201 in complex with peptide LLWNGPMAV

PDB DOI: https://doi.org/10.2210/pdb9SL0/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens, Yellow fever virus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-09-02 Released: 2025-09-17
Deposition Author(s): Liu, Y., Gfeller, D., Guillaume, P., Larabi, A., Lau, K., Pojer, F.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.264 (Depositor), 0.264 (DCC)
R-Value Work:
0.234 (Depositor), 0.234 (DCC)
R-Value Observed:
0.235 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Key determinants of T cell epitope recognition revealed by TCR specificity profiles

Liu, Y., Croce, G., Tadros, D., Moreno, D., Michel, A., Thierry, A.C., Genolet, R., Perez, M.A., Lani, R., Guillaume, P., Hebeisen, M., Teleman, M., Lau, K., Larabi, A., Racle, J., Speiser, D.E., Pojer, F., Dunn, S., Baumgaertner, P., Zoete, V., Harari, A., Gfeller, D.

(2025) bioRxiv

DOI: https://doi.org/10.1101/2025.11.17.688817

Macromolecule Content

Total Structure Weight: 45.18 kDa
Atom Count: 3,397
Modeled Residue Count: 382
Deposited Residue Count: 385
Unique protein chains: 3

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	A	276	Homo sapiens	Mutation(s): 0 Gene Names: HLA-A
UniProt
Find proteins for A5I8L1 (Homo sapiens) Explore A5I8L1 Go to UniProtKB: A5I8L1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A5I8L1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	100	Homo sapiens	Mutation(s): 0 Gene Names: B2M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769 Go to UniProtKB: P61769
PHAROS: P61769 GTEx: ENSG00000166710
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61769
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
NS5	C	9	Yellow fever virus	Mutation(s): 0
UniProt
Find proteins for W8FN10 (Yellow fever virus) Explore W8FN10 Go to UniProtKB: W8FN10
Entity Groups
UniProt Group	W8FN10
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain E [auth A] MOL2 format, chain K [auth C] MOL2 format, chain E [auth A] mmCIF format, chain K [auth C] mmCIF format, chain E [auth A]	E [auth A], K [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain K [auth C] Interactions & Density Focus chain E [auth A] Focus chain K [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], I [auth B], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain D [auth A]	D [auth A], H [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]