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T4H2 T cell receptor bound to HLA-A2 presenting GP100T2L peptide (ildqvpfsv)

Analyse T4H2 T cell receptor bound to HLA-A2 presenting GP100T2L peptide (ildqvpfsv) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6VMC
Type: protein
Length: 825 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: T4H2 T cell receptor alpha chain; T4H2 T cell receptor beta chain; MHC class I antigen…
UniProt: A0A5B8RNS7, P61769, P40967
Pockets: 12 · best druggability 0.72

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D	T4H2 T cell receptor alpha chain	protein	201	1% helix, 45% strand	—
E	T4H2 T cell receptor beta chain	protein	240	6% helix, 48% strand	—
A	MHC class I antigen, a-2 alpha chain	protein	275	27% helix, 40% strand	A0A5B8RNS7
B	Beta-2-microglobulin	protein	100	0% helix, 47% strand	P61769
C	Melanocyte protein pmel	protein	9	0% helix, 0% strand	P40967

Ligands and binding sites

GOL · Glycerol · additive · chains A

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

Pockets

12 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	1061	0.72	0.76	101	empty
2	411	0.71	0.83	51	empty
3	491	0.66	0.78	47	empty
4	124	0.46	0.78	16	empty
5	118	0.44	0.78	22	empty

Interfaces

5 interfaces between chains.

D–E · 2176 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1377 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 908 Å² buried · 12 hydrogen bonds · protein-protein
D–B · 321 Å² buried · 3 hydrogen bonds · protein-protein
D–A · 247 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

6VMC · T4H2 T cell receptor bound to HLA-A2 presenting gp100T2L peptide (ILDQVPFSV) · the same entry in another collection · chain E against E, 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
P40967 · AlphaFold monomer V2.0 prediction for melanocyte protein pmel (P40967) · a predicted model of the same protein · chain C against A, TM-score 0.44

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 P40967
Elsewhere: RCSB PDB 6VMC · PDBe 6VMC · UniProt A0A5B8RNS7 · UniProt P61769 · UniProt P40967

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