MolNFT v1 · #168239 · protein

Structure of human mait a-F7 TCR in complex with patient MR1-R9H without ligand

6W9V · Major histocompatibility complex class I-related gene…: “Structure of human mait a-F7 TCR in complex with patient MR1-R9H without ligand”. X-ray diffraction, 18 pockets (best druggability 0.80). MolNFT v1 #168239 on GenesisL1: 3D…

PDB: 6W9V
Type: protein
Length: 1,604 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
Pockets: 18 · best druggability 0.80

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, 41% strand	Q95460
B	Beta-2-microglobulin	protein	98	0% helix, 50% strand	P61769
C	Major histocompatibility complex class I-related gene protein	protein	267	27% helix, 41% strand	Q95460
D	TCR-alpha chain	protein	188	2% helix, 48% strand	—
E	TCR-beta chain	protein	241	6% helix, 51% strand	—
F	Beta-2-microglobulin	protein	100	0% helix, 51% strand	P61769
G	TCR-alpha chain	protein	201	5% helix, 45% strand	—
H	TCR-beta chain	protein	244	7% helix, 50% strand	—

Ligands and binding sites

GOL · Glycerol · additive · 4 copies · chains A, H, C, F
ACT · Acetate ion · additive · 2 copies · chains A, H

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

Pockets

18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1155	0.80	0.82	108	ACT
2	384	0.79	0.88	42	empty
3	471	0.78	0.85	49	GOL
4	1060	0.71	0.75	80	empty
5	848	0.70	0.75	76	empty

Interfaces

12 interfaces between chains.

G–H · 1986 Å² buried · 17 hydrogen bonds · protein-protein
D–E · 1845 Å² buried · 19 hydrogen bonds · protein-protein
C–F · 1342 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1282 Å² buried · 15 hydrogen bonds · protein-protein
C–H · 951 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

6W9V · Structure of human MAIT A-F7 TCR in complex with patient MR1-R9H without ligand · 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 6W9V · PDBe 6W9V · UniProt Q95460 · UniProt P61769

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