MolNFT v1 · #135698 · protein

Structure of human MR1-3-F-sa in complex with human mait a-F7 TCR

5U6Q · Major histocompatibility complex class I-related gene…: “Structure of human MR1-3-F-sa in complex with human mait a-F7 TCR”. X-ray diffraction, 2 ligands (7ZS, NA), 20 pockets (best druggability 0.78). MolNFT v1 #135698 on…

PDB: 5U6Q
Type: protein
Length: 1,598 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Major histocompatibility complex class I-related gene protein; Mait T-cell receptor alpha…
UniProt: Q95460, P61769
Ligands: 7ZS, NA
Pockets: 20 · best druggability 0.78

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	Major histocompatibility complex class I-related gene protein	protein	261	29% helix, 39% strand	Q95460
D	Mait T-cell receptor alpha chain	protein	200	5% helix, 46% strand	—
E	Mait T-cell receptor beta chain	protein	244	7% helix, 50% strand	—
F	Beta-2-microglobulin	protein	97	0% helix, 51% strand	P61769
A	Major histocompatibility complex class I-related gene protein	protein	263	28% helix, 41% strand	Q95460
B	Mait T-cell receptor alpha chain	protein	195	2% helix, 48% strand	—
G	Mait T-cell receptor beta chain	protein	239	6% helix, 50% strand	—
H	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P61769

Ligands and binding sites

7ZS · 3-methanoyl-2-oxidanyl-benzoic acid · ligand · 2 copies · chains C, D, A
NA · Sodium ion · metal · chains G
ACT · Acetate ion · additive · 2 copies · chains C, D, A, B
GOL · Glycerol · additive · chains C, D

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	840	0.78	0.81	71	empty
2	106	0.78	0.97	23	7ZS, ACT
3	372	0.75	0.85	46	7ZS, ACT
4	1158	0.72	0.76	85	empty
5	1119	0.71	0.75	82	empty

Interfaces

12 interfaces between chains.

D–E · 1965 Å² buried · 16 hydrogen bonds · protein-protein
B–G · 1919 Å² buried · 23 hydrogen bonds · protein-protein
A–H · 1321 Å² buried · 16 hydrogen bonds · protein-protein
C–F · 1214 Å² buried · 17 hydrogen bonds · protein-protein
E–A · 881 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

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

Compared structures

5U6Q · Structure of human MR1-3-F-SA in complex with human MAIT A-F7 TCR · 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 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 5U6Q · PDBe 5U6Q · UniProt Q95460 · UniProt P61769

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