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Crystal structure of TCR-MR1 ternary complex bound to 5-(2- oxoethylideneamino)-6-D-ribitylaminouracil

Analyse Crystal structure of TCR-MR1 ternary complex bound to 5-(2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4NQE
Type: protein
Length: 1,569 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; TCR…
UniProt: Q95460, P61769
Ligands: 2L4
Pockets: 14 · best druggability 0.75

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, 53% strand	P61769
C	Major histocompatibility complex class I-related gene protein	protein	249	30% helix, 40% strand	Q95460
D	TCR alpha	protein	200	5% helix, 46% strand	—
E	TCR beta	protein	243	7% helix, 51% strand	—
F	Beta-2-microglobulin	protein	97	0% helix, 51% strand	P61769
G	TCR alpha	protein	189	4% helix, 48% strand	—
H	TCR beta	protein	231	6% helix, 48% strand	—

Ligands and binding sites

2L4 · 1-deoxy-1-({2,6-dioxo-5-[(E)-(2-oxoethylidene)amino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol · ligand · 2 copies · chains A, G, H, C, D, E

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

Pockets

14 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	351	0.75	0.86	53	2L4
2	799	0.73	0.78	69	empty
3	367	0.73	0.84	53	2L4
4	1015	0.71	0.75	84	empty
5	979	0.71	0.75	81	empty

Interfaces

11 interfaces between chains.

D–E · 1987 Å² buried · 20 hydrogen bonds · protein-protein
G–H · 1939 Å² buried · 20 hydrogen bonds · protein-protein
C–F · 1206 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 1189 Å² buried · 19 hydrogen bonds · protein-protein
A–G · 675 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

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

Compared structures

4NQE · Crystal structure of TCR-MR1 ternary complex bound to… · the same entry in another collection · chain C against C, 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 4NQE · PDBe 4NQE · UniProt Q95460 · UniProt P61769

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