Research workbench

SARS-cov-2 rlq peptide binds to HLA-A2

Analyse SARS-cov-2 rlq peptide binds to HLA-A2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7N1B
Type: protein
Length: 764 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MHC class I antigen, a-2 alpha chain; Beta-2-microglobulin; Spike protein S2
UniProt: A0A5B8RNS7, P61769, P0DTC2
Pockets: 10 · best druggability 0.76

Structure

x-ray diffraction · 4 distinct chains · 22% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MHC class I antigen, a-2 alpha chain	protein	274	27% helix, 40% strand	A0A5B8RNS7
B, E	Beta-2-microglobulin	protein	100	0% helix, 51% strand	P61769
C, F	Spike protein S2	protein	9	0% helix, 0% strand	P0DTC2
D	MHC class I antigen, a-2 alpha chain	protein	272	26% helix, 36% strand	A0A5B8RNS7

Pockets

10 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	91	0.76	0.97	18	empty
2	619	0.71	0.79	58	empty
3	583	0.70	0.79	56	empty
4	574	0.64	0.75	61	empty
5	173	0.51	0.78	40	empty

Interfaces

8 interfaces between chains.

A–B · 1405 Å² buried · 18 hydrogen bonds · protein-protein
D–E · 1363 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 925 Å² buried · 16 hydrogen bonds · protein-protein
D–F · 916 Å² buried · 16 hydrogen bonds · protein-protein
A–D · 184 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

7N1B · SARS-CoV-2 RLQ peptide binds to HLA-A2 · 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 A0A5B8RNS7
Every structure of UniProt P61769
Every structure of UniProt P0DTC2
Elsewhere: RCSB PDB 7N1B · PDBe 7N1B · UniProt A0A5B8RNS7 · UniProt P61769 · UniProt P0DTC2

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