9SKO | pdb_00009sko

Crystal structure of HLA-A0201 in complex with peptide LLWNGPMAVS

PDB DOI: https://doi.org/10.2210/pdb9SKO/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: 1.49 Å
R-Value Free:
0.204 (Depositor), 0.204 (DCC)
R-Value Work:
0.184 (Depositor), 0.184 (DCC)
R-Value Observed:
0.185 (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: 46.82 kDa
Atom Count: 3,526
Modeled Residue Count: 383
Deposited Residue Count: 386
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
LLWNGPMAVS peptide	C	10	Yellow fever virus	Mutation(s): 0
UniProt
Find proteins for P03314 (Yellow fever virus (strain 17D vaccine)) Explore P03314 Go to UniProtKB: P03314
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03314
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain Z [auth B]	Z [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain Z [auth B] Interactions & Density Focus chain Z [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain E [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain E [auth A] mmCIF format, chain BA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain E [auth A]	BA [auth B], E [auth A], P [auth A], Q [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain E [auth A] Focus chain P [auth A] Focus chain Q [auth A] Interactions & Density Focus chain BA [auth B] Focus chain E [auth A] Focus chain P [auth A] Focus chain Q [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain V [auth A] SDF format, chain DA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain V [auth A] MOL2 format, chain DA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain V [auth A] mmCIF format, chain DA [auth B]	DA [auth B] G [auth A] R [auth A] S [auth A] T [auth A] DA [auth B], G [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain DA [auth B] Focus chain G [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Interactions & Density Focus chain DA [auth B] Focus chain G [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain F [auth A] SDF format, chain GA [auth B] SDF format, chain I [auth A] SDF format, chain IA [auth B] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain JA [auth C] SDF format, chain J [auth A] SDF format, chain CA [auth B] SDF format, chain AA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] CA [auth B] EA [auth B] F [auth A] GA [auth B] AA [auth B], CA [auth B], EA [auth B], F [auth A], GA [auth B], I [auth A], IA [auth B], J [auth A], JA [auth C], L [auth A], M [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth B] Focus chain CA [auth B] Focus chain EA [auth B] Focus chain F [auth A] Focus chain GA [auth B] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth C] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain AA [auth B] Focus chain CA [auth B] Focus chain EA [auth B] Focus chain F [auth A] Focus chain GA [auth B] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth C] Focus chain L [auth A] Focus chain M [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain FA [auth B] SDF format, chain HA [auth B] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain LA [auth C] SDF format, chain O [auth A] SDF format, chain N [auth A] MOL2 format, chain D [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] mmCIF format, chain D [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain LA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A]	D [auth A] FA [auth B] HA [auth B] K [auth A] KA [auth C] D [auth A], FA [auth B], HA [auth B], K [auth A], KA [auth C], LA [auth C], N [auth A], O [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain FA [auth B] Focus chain HA [auth B] Focus chain K [auth A] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain D [auth A] Focus chain FA [auth B] Focus chain HA [auth B] Focus chain K [auth A] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain N [auth A] Focus chain O [auth A]