Research workbench

Newly identified epitope MN2 from SARS-cov M protein complexed withhla-A*0201

Analyse Newly identified epitope MN2 from SARS-cov M protein complexed withhla-A*0201 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3I6G
Type: protein
Length: 768 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; Membrane…
UniProt: P01892, P61769, P59596
Pockets: 12 · best druggability 0.69

Structure

x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	HLA class I histocompatibility antigen, a-2 alpha chain	protein	275	27% helix, 40% strand	P01892
B, E	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C, F	Membrane protein	protein	9	0% helix, 0% strand	P59596

Pockets

12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	674	0.69	0.77	56	empty
2	584	0.65	0.76	54	empty
3	160	0.64	0.85	26	empty
4	147	0.51	0.79	28	empty
5	172	0.50	0.78	21	empty

Interfaces

7 interfaces between chains.

D–E · 1377 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1325 Å² buried · 15 hydrogen bonds · protein-protein
A–C · 890 Å² buried · 13 hydrogen bonds · protein-protein
D–F · 883 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 627 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

3I6G · Newly identified epitope Mn2 from SARS-CoV M protein complexed withHLA-A*0201 · 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 0.98

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 P59596
Elsewhere: RCSB PDB 3I6G · PDBe 3I6G · UniProt P01892 · UniProt P61769 · UniProt P59596

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