MolNFT v1 · #182705 · protein

SARS-cov-2 ylq peptide-specific TCR PYLQ7 binds to ylq-HLA-A2

7N1F · PYLQ7 T cell receptor alpha chain: “SARS-cov-2 ylq peptide-specific TCR PYLQ7 binds to ylq-HLA-A2”. X-ray diffraction, 11 pockets (best druggability 0.77). MolNFT v1 #182705 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 7N1F
Type: protein
Length: 818 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: PYLQ7 T cell receptor alpha chain; PYLQ7 T cell receptor beta chain; MHC class I antigen…
UniProt: A0A5B8RNS7, P61769, P0DTC2
Pockets: 11 · best druggability 0.77

Structure

x-ray diffraction · 5 distinct chains · 11% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D	PYLQ7 T cell receptor alpha chain	protein	197	2% helix, 42% strand	—
E	PYLQ7 T cell receptor beta chain	protein	240	8% helix, 50% strand	—
A	MHC class I antigen, a-2 alpha chain	protein	272	26% helix, 38% strand	A0A5B8RNS7
B	Beta-2-microglobulin	protein	100	0% helix, 51% strand	P61769
C	Spike protein S1	protein	9	0% helix, 0% strand	P0DTC2

Pockets

11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1031	0.77	0.80	89	empty
2	571	0.67	0.77	58	empty
3	173	0.51	0.78	29	empty
4	112	0.44	0.78	23	empty
5	72	0.44	0.81	17	empty

Interfaces

7 interfaces between chains.

D–E · 2157 Å² buried · 29 hydrogen bonds · protein-protein
A–B · 1377 Å² buried · 24 hydrogen bonds · protein-protein
A–C · 911 Å² buried · 15 hydrogen bonds · protein-protein
D–A · 509 Å² buried · 8 hydrogen bonds · protein-protein
E–A · 307 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

7N1F · SARS-CoV-2 YLQ peptide-specific TCR pYLQ7 binds to YLQ-HLA-A2 · the same entry in another collection · chain D against D, 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 A0A5B8RNS7
Every structure of UniProt P61769
Every structure of UniProt P0DTC2
Elsewhere: RCSB PDB 7N1F · PDBe 7N1F · UniProt A0A5B8RNS7 · UniProt P61769 · UniProt P0DTC2

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