MolNFT v1 · #118198 · protein

PF6-M1-HLA-A2

5EUO · HLA class I histocompatibility antigen, a-2 alpha chain: “PF6-M1-HLA-A2”. X-ray diffraction, 19 pockets (best druggability 0.70). MolNFT v1 #118198 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5EUO
Type: protein
Length: 1,624 residues
Chains: 10
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; PF6 TCR…
UniProt: P01892, P61769, P03485
Pockets: 19 · best druggability 0.70

Structure

x-ray diffraction · 8 distinct chains · 12% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HLA class I histocompatibility antigen, a-2 alpha chain	protein	274	27% helix, 36% strand	P01892
B, D	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C	HLA class I histocompatibility antigen, a-2 alpha chain	protein	275	27% helix, 40% strand	P01892
E	PF6 TCR alpha chain	protein	190	2% helix, 48% strand	—
F	PF6 TCR beta chain	protein	239	6% helix, 48% strand	—
G	PF6 TCR alpha chain	protein	191	3% helix, 47% strand	—
H	PF6 TCR beta chain	protein	237	5% helix, 49% strand	—
I, J	Matrix protein 1	protein	9	0% helix, 0% strand	P03485

Ligands and binding sites

IMD · Imidazole · additive · 2 copies · chains C, G, H

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

Pockets

19 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	835	0.70	0.76	72	empty
2	688	0.70	0.77	59	empty
3	890	0.70	0.75	97	IMD
4	924	0.70	0.75	81	empty
5	223	0.51	0.76	35	empty

Interfaces

15 interfaces between chains.

G–H · 2059 Å² buried · 20 hydrogen bonds · protein-protein
E–F · 2018 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 1377 Å² buried · 26 hydrogen bonds · protein-protein
C–D · 1339 Å² buried · 23 hydrogen bonds · protein-protein
A–J · 851 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

5EUO · PF6-M1-HLA-A2 · the same entry in another collection · chain J against J, TM-score 1.00
P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain D against A, TM-score 0.98

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
Every structure of UniProt P03485
Elsewhere: RCSB PDB 5EUO · PDBe 5EUO · UniProt P01892 · UniProt P61769 · UniProt P03485

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