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Complex structure of HLA0201 with recognizing SARS-cov-2 epitope S1

Analyse Complex structure of HLA0201 with recognizing SARS-cov-2 epitope S1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7EU2
Type: protein
Length: 776 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MHC class I antigen; Beta-2-microglobulin; SARS-cov-2 T-cell epitope S1
UniProt: A0A5H2UU57, P61769
Pockets: 9 · best druggability 0.78

Structure

x-ray diffraction · 5 distinct chains · 19% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MHC class I antigen	protein	280	25% helix, 39% strand	A0A5H2UU57
B	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C, F	SARS-cov-2 T-cell epitope S1	protein	9	0% helix, 0% strand	—
D	MHC class I antigen	protein	279	26% helix, 40% strand	A0A5H2UU57
E	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P61769

Pockets

9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	867	0.78	0.81	81	empty
2	507	0.73	0.82	55	empty
3	55	0.46	0.84	17	empty
4	119	0.45	0.78	17	empty
5	88	0.43	0.79	20	empty

Interfaces

5 interfaces between chains.

A–D · 1603 Å² buried · 37 hydrogen bonds · protein-protein
D–E · 1335 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1329 Å² buried · 16 hydrogen bonds · protein-protein
D–F · 915 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 905 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

7EU2 · Complex structure of HLA0201 with recognizing SARS-CoV-2 epitope S1 · 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 E 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 A0A5H2UU57
Every structure of UniProt P61769
Elsewhere: RCSB PDB 7EU2 · PDBe 7EU2 · UniProt A0A5H2UU57 · UniProt P61769

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