MolNFT v1 · #118179 · protein

HLA class I antigen

5EU4 · HLA class I histocompatibility antigen, a-2 alpha chain: “HLA class I antigen”. X-ray diffraction, 1 ligand (SO4), 9 pockets (best druggability 0.76). MolNFT v1 #118179 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5EU4
Type: protein
Length: 770 residues
Chains: 6
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; Peptide…
UniProt: P01892, P61769
Ligands: SO4
Pockets: 9 · best druggability 0.76

Structure

x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	HLA class I histocompatibility antigen, a-2 alpha chain	protein	276	26% helix, 40% strand	P01892
B, E	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C, F	Peptide antigen ylapgpvta	protein	9	0% helix, 0% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 7 copies · chains A, D, B, E
EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, C, D, F, E
GOL · Glycerol · additive · chains A, B

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

Pockets

9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1072	0.76	0.79	84	SO4
2	521	0.71	0.80	51	SO4
3	698	0.70	0.77	56	GOL, SO4
4	317	0.57	0.76	46	SO4
5	68	0.55	0.87	15	EDO

Interfaces

7 interfaces between chains.

A–B · 1363 Å² buried · 27 hydrogen bonds · protein-protein
D–E · 1326 Å² buried · 23 hydrogen bonds · protein-protein
D–F · 793 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 791 Å² buried · 13 hydrogen bonds · protein-protein
A–D · 588 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

5EU4 · HLA Class I antigen · the same entry in another collection · chain F against F, 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 5EU4 · PDBe 5EU4 · UniProt P01892 · UniProt P61769

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