MolNFT v1 · #114791 · protein

1E6 TCR in complex with HLA-A02 carrying rqfgpdfpti

5C0B · HLA class I histocompatibility antigen, a-2 alpha chain: “1E6 TCR in complex with HLA-A02 carrying rqfgpdfpti”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.79). MolNFT v1 #114791 on GenesisL1: 3D structure…

PDB: 5C0B
Type: protein
Length: 1,657 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; Marker…
UniProt: P01892, P61769
Ligands: SO4
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 7 distinct chains · 10% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F	HLA class I histocompatibility antigen, a-2 alpha chain	protein	275	27% helix, 40% strand	P01892
B, G	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
C, H	Marker peptide	protein	10	0% helix, 0% strand	—
D	1E6 TCR alpha chain	protein	197	2% helix, 45% strand	—
E	1E6 TCR beta chain	protein	247	9% helix, 51% strand	—
I	1E6 TCR alpha chain	protein	199	4% helix, 45% strand	—
J	1E6 TCR beta chain	protein	244	9% helix, 52% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 8 copies · chains A, B, D, E, F, G
EDO · 1,2-ethanediol · additive · 55 copies · chains A, C, D, F, B, E, G, H, J, I
GOL · Glycerol · additive · 6 copies · chains A, B, D, E, F, G, I, J
PG4 · Tetraethylene glycol · additive · chains I, J

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	619	0.79	0.84	75	EDO
2	956	0.75	0.78	92	EDO, GOL
3	1185	0.72	0.76	100	EDO, PG4
4	583	0.68	0.78	54	EDO
5	629	0.68	0.77	56	GOL

Interfaces

18 interfaces between chains.

D–E · 2299 Å² buried · 26 hydrogen bonds · protein-protein
I–J · 2277 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 1414 Å² buried · 28 hydrogen bonds · protein-protein
F–G · 1382 Å² buried · 26 hydrogen bonds · protein-protein
A–C · 956 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

5C0B · 1E6 TCR in complex with HLA-A02 carrying RQFGPDFPTI · 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 0.99

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 P01892
Every structure of UniProt P61769
Elsewhere: RCSB PDB 5C0B · PDBe 5C0B · UniProt P01892 · UniProt P61769

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