MolNFT v1 · #160783 · protein

Structure of human mait a-F7 TCR in complex with human MR1-5-op-ru

6PUC · Major histocompatibility complex class I-related gene…: “Structure of human mait a-F7 TCR in complex with human MR1-5-op-ru”. X-ray diffraction, 3 ligands (Q87, NA, CL), 16 pockets (best druggability 0.81). MolNFT v1 #160783 on…

PDB: 6PUC
Type: protein
Length: 1,601 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…
UniProt: Q95460, P61769
Ligands: Q87, NA, CL
Pockets: 16 · best druggability 0.81

Structure

x-ray diffraction · 8 distinct chains · 12% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Major histocompatibility complex class I-related gene protein	protein	265	28% helix, 40% strand	Q95460
B	Beta-2-microglobulin	protein	98	0% helix, 52% strand	P61769
C	Major histocompatibility complex class I-related gene protein	protein	267	27% helix, 41% strand	Q95460
D	Human TCR alpha chain	protein	188	2% helix, 49% strand	—
E	Human TCR beta chain	protein	241	6% helix, 51% strand	—
F	Beta-2-microglobulin	protein	99	0% helix, 52% strand	P61769
G	Human TCR alpha chain	protein	199	4% helix, 45% strand	—
H	Human TCR beta chain	protein	244	7% helix, 50% strand	—

Ligands and binding sites

Q87 · 1-deoxy-1-({2,6-dioxo-5-[(E)-(2-oxopropylidene)amino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol · ligand · 2 copies · chains A, G, H, C, D, E
NA · Sodium ion · metal · 2 copies · chains F, H
CL · Chloride ion · ion · 2 copies · chains A, F
GOL · Glycerol · additive · 3 copies · chains A, H, C, F

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

Pockets

16 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	1059	0.81	0.82	105	empty
2	314	0.75	0.86	49	Q87
3	368	0.73	0.84	54	Q87
4	1031	0.72	0.75	78	empty
5	750	0.70	0.76	81	CL

Interfaces

12 interfaces between chains.

G–H · 2015 Å² buried · 18 hydrogen bonds · protein-protein
D–E · 1930 Å² buried · 23 hydrogen bonds · protein-protein
C–F · 1296 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 1252 Å² buried · 16 hydrogen bonds · protein-protein
C–H · 963 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

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

Compared structures

6PUC · Structure of human MAIT A-F7 TCR in complex with human MR1-5-OP-RU · 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 B 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 6PUC · PDBe 6PUC · UniProt Q95460 · UniProt P61769

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