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Structure of human mait TCR in complex with human MR1-6-fp

Analyse Structure of human mait TCR in complex with human MR1-6-fp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4L4T
Type: protein
Length: 1,585 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Major histocompatibility complex class I-related gene protein; Beta-2-microglobulin; Mait…
UniProt: Q95460, P61769
Ligands: 6FP
Pockets: 16 · best druggability 0.74

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	264	28% helix, 41% strand	Q95460
B	Beta-2-microglobulin	protein	96	0% helix, 51% strand	P61769
C	Major histocompatibility complex class I-related gene protein	protein	250	29% helix, 40% strand	Q95460
D	Mait T-cell receptor alpha chain	protein	200	5% helix, 45% strand	—
E	Mait T-cell receptor beta chain	protein	243	7% helix, 49% strand	—
F	Beta-2-microglobulin	protein	97	0% helix, 51% strand	P61769
G	Mait T-cell receptor alpha chain	protein	193	3% helix, 48% strand	—
H	Mait T-cell receptor beta chain	protein	242	6% helix, 50% strand	—

Ligands and binding sites

6FP · 2-amino-4-oxo-3,4-dihydropteridine-6-carbaldehyde · ligand · 2 copies · chains A, G, C, D

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

Pockets

16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	315	0.74	0.86	50	6FP
2	799	0.74	0.78	68	empty
3	1060	0.72	0.76	86	empty
4	383	0.72	0.83	54	6FP
5	1010	0.72	0.76	77	empty

Interfaces

11 interfaces between chains.

D–E · 2023 Å² buried · 18 hydrogen bonds · protein-protein
G–H · 2020 Å² buried · 23 hydrogen bonds · protein-protein
C–F · 1218 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1161 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 662 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

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

Compared structures

4L4T · Structure of human MAIT TCR in complex with human MR1-6-FP · the same entry in another collection · chain H against H, TM-score 1.00
Q95460 · AlphaFold monomer V2.0 prediction for major histocompatibility complex class I-related… · a predicted model of the same protein · chain C against A, TM-score 0.99
P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain F 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 4L4T · PDBe 4L4T · UniProt Q95460 · UniProt P61769

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