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 1.1 of the entry. See complete history.

Literature

Crystal structure of HLA-A0201 in complex with peptide LLWNGPMAVS

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

To be published.

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:

(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A5I8L1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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 E [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain BA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [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 DA [auth B] 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 V [auth A] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth A] MOL2 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 V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] mmCIF 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 V [auth A] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A] mmCIF format, chain Y [auth A]	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 AA [auth B] SDF format, chain CA [auth B] 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 J [auth A] SDF format, chain JA [auth C] SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain CA [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 J [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain CA [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 J [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A]	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 N [auth A] SDF format, chain O [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 N [auth A] MOL2 format, chain O [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 N [auth A] mmCIF format, chain O [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]