Research workbench

Crystal structure of HLA-A*0201 in complex with SARS-cov-2 N226-234

Analyse Crystal structure of HLA-A*0201 in complex with SARS-cov-2 N226-234 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7KGT
Type: protein
Length: 380 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MHC class I antigen; Beta-2-microglobulin; Nucleoprotein
UniProt: Q861F7, P61769, P0DTC9
Ligands: CD, NA
Pockets: 5 · best druggability 0.68

Structure

x-ray diffraction · 3 distinct chains · 19% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MHC class I antigen	protein	278	26% helix, 40% strand	Q861F7
B	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P61769
C	Nucleoprotein	protein	3	0% helix, 0% strand	P0DTC9

Ligands and binding sites

CD · Cadmium ion · metal · 2 copies · chains A
NA · Sodium ion · metal · chains A
ACT · Acetate ion · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	620	0.68	0.77	56	empty
2	56	0.40	0.81	15	empty
3	94	0.39	0.77	18	empty
4	98	0.38	0.75	14	empty
5	51	0.34	0.78	15	empty

Interfaces

2 interfaces between chains.

A–B · 1276 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 425 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

7KGT · Crystal Structure of HLA-A*0201 in complex with SARS-CoV-2 N226-234 · 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 Q861F7
Every structure of UniProt P61769
Every structure of UniProt P0DTC9
Elsewhere: RCSB PDB 7KGT · PDBe 7KGT · UniProt Q861F7 · UniProt P61769 · UniProt P0DTC9

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