MolNFT v1 · #160788 · protein

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

6PUH · Major histocompatibility complex class I-related gene…: “Structure of human mait a-F7 TCR in complex with human MR1-ribityl- less”. X-ray diffraction, 2 ligands (OYG, NA), 20 pockets (best druggability 0.81). MolNFT v1 #160788 on…

PDB: 6PUH
Type: protein
Length: 1,610 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Major histocompatibility complex class I-related gene protein; Human TCR alpha chain…
UniProt: Q95460, P61769
Ligands: OYG, 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	265	29% helix, 40% strand	Q95460
B	Human TCR alpha chain	protein	199	5% helix, 46% strand	—
C	Major histocompatibility complex class I-related gene protein	protein	268	27% helix, 41% strand	Q95460
D	Human TCR alpha chain	protein	194	3% helix, 48% strand	—
E	Human TCR beta chain	protein	242	6% helix, 51% strand	—
F	Beta-2-microglobulin	protein	100	0% helix, 51% strand	P61769
G	Human TCR beta chain	protein	244	7% helix, 50% strand	—
H	Beta-2-microglobulin	protein	98	0% helix, 50% strand	P61769

Ligands and binding sites

OYG · 6-methyl-5-[(1E)-3-oxobut-1-en-1-yl]pyrimidine-2,4(1H, 3H)-dione · ligand · 2 copies · chains A, C
NA · Sodium ion · metal · 2 copies · chains F, G

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

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1122	0.81	0.83	100	empty
2	113	0.78	0.97	25	OYG
3	414	0.77	0.86	54	OYG
4	1024	0.71	0.75	90	empty
5	999	0.71	0.75	74	empty

Interfaces

12 interfaces between chains.

B–G · 2008 Å² buried · 21 hydrogen bonds · protein-protein
D–E · 1976 Å² buried · 25 hydrogen bonds · protein-protein
C–F · 1351 Å² buried · 16 hydrogen bonds · protein-protein
A–H · 1265 Å² buried · 17 hydrogen bonds · protein-protein
C–G · 990 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

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

Compared structures

6PUH · Structure of human MAIT A-F7 TCR in complex with human MR1-Ribityl-less · 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 6PUH · PDBe 6PUH · UniProt Q95460 · UniProt P61769

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