MolNFT v1 · #121538 · protein

1E6 TCR in complex with HLA-A02 carrying aqwgpdpaaa

5HYJ · HLA class I histocompatibility antigen, a-2 alpha chain: “1E6 TCR in complex with HLA-A02 carrying aqwgpdpaaa”. X-ray diffraction, 20 pockets (best druggability 0.76). MolNFT v1 #121538 on GenesisL1: 3D structure, binding sites and…

PDB: 5HYJ
Type: protein
Length: 1,650 residues
Chains: 10
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…
UniProt: P01892, P61769
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 5 distinct chains · 12% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F	HLA class I histocompatibility antigen, a-2 alpha chain	protein	276	26% helix, 36% strand	P01892
B, G	Beta-2-microglobulin	protein	100	0% helix, 45% strand	P61769
C, H	Ala-gln-TRP-gly-pro-asp-pro-ala-ala-ala	protein	10	0% helix, 0% strand	—
D, I	Human T-cell receptor, class I, light alpha chain	protein	193	3% helix, 44% strand	—
E, J	Human T-cell receptor, class I, heavy beta chain	protein	246	8% helix, 49% strand	—

Pockets

20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1035	0.76	0.78	92	empty
2	1138	0.72	0.76	81	empty
3	500	0.68	0.79	45	empty
4	575	0.68	0.78	54	empty
5	566	0.65	0.76	57	empty

Interfaces

17 interfaces between chains.

I–J · 2412 Å² buried · 27 hydrogen bonds · protein-protein
D–E · 2408 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 1493 Å² buried · 18 hydrogen bonds · protein-protein
F–G · 1446 Å² buried · 15 hydrogen bonds · protein-protein
D–I · 845 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

5HYJ · 1E6 TCR in Complex with HLA-A02 carrying AQWGPDPAAA · the same entry in another collection · chain J against J, TM-score 1.00
P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain G 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
Elsewhere: RCSB PDB 5HYJ · PDBe 5HYJ · UniProt P01892 · UniProt P61769

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