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Crystal structure of a human autoimmune TCR MS2-3C8 bound to MHC class II self-ligand MBP/HLA-DR4

Analyse Crystal structure of a human autoimmune TCR MS2-3C8 bound to MHC class II… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3O6F
Type: protein
Length: 1,629 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HLA class II histocompatibility antigen, dr alpha chain; HLA class II histocompatibility…
UniProt: P01903, P13760, P01848, A0A5B9
Pockets: 20 · best druggability 0.71

Structure

x-ray diffraction · 8 distinct chains · 9% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HLA class II histocompatibility antigen, dr alpha chain	protein	178	13% helix, 42% strand	P01903
B	HLA class II histocompatibility antigen, DRB1-4 beta chain	protein	195	17% helix, 39% strand	P13760
C	T-cell receptor alpha chain C region	protein	191	2% helix, 40% strand	P01848
D	T-cell receptor beta-1 chain C region	protein	245	7% helix, 49% strand	A0A5B9
E	HLA class II histocompatibility antigen, dr alpha chain	protein	179	13% helix, 45% strand	P01903
F	HLA class II histocompatibility antigen, DRB1-4 beta chain	protein	210	15% helix, 38% strand	P13760
G	T-cell receptor alpha chain C region	protein	188	2% helix, 40% strand	P01848
H	T-cell receptor beta-1 chain C region	protein	243	5% helix, 47% strand	A0A5B9

Pockets

20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1033	0.71	0.75	79	empty
2	1027	0.70	0.74	84	empty
3	103	0.69	0.92	22	empty
4	655	0.65	0.75	69	empty
5	465	0.62	0.76	40	empty

Interfaces

17 interfaces between chains.

E–F · 3165 Å² buried · 56 hydrogen bonds · protein-protein
A–B · 2987 Å² buried · 59 hydrogen bonds · protein-protein
G–H · 2132 Å² buried · 26 hydrogen bonds · protein-protein
C–D · 2110 Å² buried · 26 hydrogen bonds · protein-protein
A–D · 516 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide (disulfide).

Compared structures

3O6F · Crystal structure of a human autoimmune TCR MS2-3C8 bound to MHC class II self-ligand… · the same entry in another collection · chain H against H, TM-score 1.00
P01903 · AlphaFold monomer V2.0 prediction for HLA class II histocompatibility antigen, dr alpha… · a predicted model of the same protein · chain A against A, TM-score 0.95
A0A5B9 · AlphaFold monomer V2.0 prediction for T cell receptor beta constant 2 (A0A5B9) · a predicted model of the same protein · chain D against A, TM-score 0.53

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 P01903
Every structure of UniProt P13760
Every structure of UniProt P01848
Every structure of UniProt A0A5B9
Elsewhere: RCSB PDB 3O6F · PDBe 3O6F · UniProt P01903 · UniProt P13760 · UniProt P01848 · UniProt A0A5B9

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