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Structure of human mait a-F7 TCR in complex with human MR1-JYM72

Analyse Structure of human mait a-F7 TCR in complex with human MR1-JYM72 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6PUK
Type: protein
Length: 1,613 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Major histocompatibility complex class I-related gene protein; Tra@ protein; Human TCR…
UniProt: Q95460, P61769
Ligands: OYV, NA
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 8 distinct chains · 12% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Major histocompatibility complex class I-related gene protein	protein	266	27% helix, 40% strand	Q95460
B	Tra@ protein	protein	201	3% helix, 45% strand	—
C	Major histocompatibility complex class I-related gene protein	protein	266	28% helix, 41% strand	Q95460
D	Tra@ protein	protein	196	3% helix, 47% strand	—
E	Human TCR beta chain	protein	243	6% helix, 50% strand	—
F	Beta-2-microglobulin	protein	99	0% helix, 52% strand	P61769
G	Human TCR beta chain	protein	244	7% helix, 49% strand	—
H	Beta-2-microglobulin	protein	98	0% helix, 50% strand	P61769

Ligands and binding sites

OYV · 1,2-dideoxy-1-{2,6-dioxo-5-[(1E)-3-oxobut-1-en-1-yl]-1, 2,3,6-tetrahydropyrimidin-4-yl}-D-ribo-hexitol · ligand · 2 copies · chains A, B, C, D
NA · Sodium ion · metal · 3 copies · chains F, G, H
GOL · Glycerol · additive · 3 copies · chains A, G, C, F
ACT · Acetate ion · additive · chains F

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

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1053	0.81	0.82	98	empty
2	413	0.77	0.86	53	OYV
3	413	0.76	0.85	47	OYV
4	1049	0.71	0.75	90	empty
5	905	0.69	0.75	77	empty

Interfaces

12 interfaces between chains.

B–G · 2073 Å² buried · 23 hydrogen bonds · protein-protein
D–E · 1988 Å² buried · 23 hydrogen bonds · protein-protein
C–F · 1289 Å² buried · 17 hydrogen bonds · protein-protein
A–H · 1255 Å² buried · 17 hydrogen bonds · protein-protein
C–G · 879 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide, 2 covalent (disulfide, covalent ligand).

Compared structures

6PUK · Structure of human MAIT A-F7 TCR in complex with human MR1-JYM72 · the same entry in another collection · chain H against H, TM-score 1.00
P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain H 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 Q95460
Every structure of UniProt P61769
Elsewhere: RCSB PDB 6PUK · PDBe 6PUK · UniProt Q95460 · UniProt P61769

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