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HLA class I antigen

Analyse HLA class I antigen in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5EU6
Type: protein
Length: 833 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class I histocompatibility antigen, a-2 alpha chain; Beta-2-microglobulin…
UniProt: P01892, P61769
Ligands: SO4
Pockets: 13 · best druggability 0.70

Structure

x-ray diffraction · 5 distinct chains · 11% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HLA class I histocompatibility antigen, a-2 alpha chain	protein	276	26% helix, 39% strand	P01892
B	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C	Tyr-leu-glu-pro-gly-pro-val-thr-val	protein	9	0% helix, 0% strand	—
D	Human TCR light chain	protein	204	1% helix, 44% strand	—
E	Human TCR heavy chain	protein	244	7% helix, 48% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 8 copies · chains A, B, E
EDO · 1,2-ethanediol · additive · 10 copies · chains A, B, E, D
GOL · Glycerol · additive · 3 copies · chains A, D, E

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	901	0.70	0.75	74	GOL, SO4
2	657	0.70	0.78	56	empty
3	184	0.63	0.84	28	empty
4	228	0.49	0.75	30	GOL
5	167	0.47	0.76	27	EDO, SO4

Interfaces

7 interfaces between chains.

D–E · 1905 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 1434 Å² buried · 23 hydrogen bonds · protein-protein
A–C · 842 Å² buried · 16 hydrogen bonds · protein-protein
A–E · 539 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 319 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

5EU6 · HLA Class I antigen · the same entry in another collection · chain A against A, TM-score 1.00
P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.99

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P01892
Every structure of UniProt P61769
Elsewhere: RCSB PDB 5EU6 · PDBe 5EU6 · UniProt P01892 · UniProt P61769

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