MolNFT v1 · #141150 · protein

An affinity enhanced T cell receptor in complex with HLA-A0201 restricted HCV NS3 peptide klvalginav

5YXU · T cell receptor alpha chain: “An affinity enhanced T cell receptor in complex with HLA-A0201 restricted HCV NS3 peptide klvalginav”. X-ray diffraction, 20 pockets (best druggability 0.83). MolNFT v1 #141150 on GenesisL1: 3D…

PDB: 5YXU
Type: protein
Length: 1,632 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: T cell receptor alpha chain; T cell receptor beta chain; HLA class I histocompatibility…
UniProt: P01892
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 9 distinct chains · 12% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
F	T cell receptor alpha chain	protein	190	3% helix, 42% strand	—
G	T cell receptor beta chain	protein	239	7% helix, 46% strand	—
A	T cell receptor alpha chain	protein	191	3% helix, 43% strand	—
B	T cell receptor beta chain	protein	242	7% helix, 46% strand	—
C	HLA class I histocompatibility antigen, a-2 alpha chain	protein	275	27% helix, 39% strand	P01892
D	Beta-2-microglobulin	protein	100	0% helix, 49% strand	—
E	HLA class I histocompatibility antigen, a-2 alpha chain	protein	276	25% helix, 37% strand	P01892
H	Beta-2-microglobulin	protein	99	0% helix, 47% strand	—
I, J	Lys-leu-val-ala-leu-gly-ile-asn-ala-val	protein	10	0% helix, 0% strand	—

Pockets

20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	686	0.83	0.87	70	empty
2	989	0.77	0.79	91	empty
3	906	0.72	0.77	84	empty
4	651	0.68	0.77	56	empty
5	220	0.53	0.77	28	empty

Interfaces

17 interfaces between chains.

F–G · 2379 Å² buried · 27 hydrogen bonds · protein-protein
A–B · 2317 Å² buried · 26 hydrogen bonds · protein-protein
C–D · 1400 Å² buried · 18 hydrogen bonds · protein-protein
E–H · 1282 Å² buried · 17 hydrogen bonds · protein-protein
E–J · 865 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

5YXU · an affinity enhanced T cell receptor in complex with HLA-A0201 restricted HCV NS3 peptide… · the same entry in another collection · chain F against F, TM-score 1.00

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
Elsewhere: RCSB PDB 5YXU · PDBe 5YXU · UniProt P01892

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