Research workbench

TCR F50 recgonizing M1-HLA-A2

Analyse TCR F50 recgonizing M1-HLA-A2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5TEZ
Type: protein
Length: 826 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gly-ile-leu-gly-phe-val-phe-thr-leu; HLA class I histocompatibility antigen, a-2 alpha…
UniProt: P01892, P61769
Pockets: 11 · best druggability 0.76

Structure

x-ray diffraction · 5 distinct chains · 12% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	Gly-ile-leu-gly-phe-val-phe-thr-leu	protein	9	0% helix, 0% strand	—
A	HLA class I histocompatibility antigen, a-2 alpha chain	protein	275	27% helix, 40% strand	P01892
B	Beta-2-microglobulin	protein	100	0% helix, 49% strand	P61769
I	TCR F50 alpha chain	protein	202	4% helix, 50% strand	—
J	TCR F50 beta chain	protein	240	7% helix, 50% strand	—

Pockets

11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	910	0.76	0.79	71	empty
2	635	0.69	0.78	53	empty
3	208	0.51	0.77	23	empty
4	169	0.51	0.78	27	empty
5	127	0.48	0.79	23	empty

Interfaces

7 interfaces between chains.

I–J · 2285 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 1368 Å² buried · 24 hydrogen bonds · protein-protein
C–A · 796 Å² buried · 10 hydrogen bonds · protein-protein
A–J · 428 Å² buried · 3 hydrogen bonds · protein-protein
A–I · 375 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

5TEZ · TCR F50 recgonizing M1-HLA-A2 · the same entry in another collection · chain C against C, 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 0.98

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 5TEZ · PDBe 5TEZ · UniProt P01892 · UniProt P61769

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