Research workbench

Crystal structure of HLA-A*0201IN complex with SARS-cov-2 N159-167

Analyse Crystal structure of HLA-A*0201IN complex with SARS-cov-2 N159-167 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7KGR
Type: protein
Length: 381 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
Pockets: 5 · best druggability 0.69

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	274	27% helix, 41% strand	Q861F7
B	Beta-2-microglobulin	protein	98	0% helix, 50% strand	P61769
C	Nucleoprotein	protein	9	0% helix, 0% strand	P0DTC9

Pockets

5 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	697	0.69	0.77	57	empty
2	79	0.57	0.88	20	empty
3	94	0.41	0.77	17	empty
4	68	0.33	0.75	13	empty
5	50	0.32	0.77	17	empty

Interfaces

2 interfaces between chains.

A–B · 1307 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 833 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

7KGR · Crystal Structure of HLA-A*0201in complex with SARS-CoV-2 N159-167 · 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 7KGR · PDBe 7KGR · UniProt Q861F7 · UniProt P61769 · UniProt P0DTC9

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