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Crystal structure of TCR-MR1 ternary complex and non-covalently bound 5-(2-oxopropylideneamino)-6-D-ribitylaminouracil

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

PDB: 4NQD
Type: protein
Length: 1,576 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: 2LJ
Pockets: 14 · best druggability 0.76

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	260	29% helix, 41% strand	Q95460
B	Beta-2-microglobulin	protein	96	0% helix, 51% strand	P61769
C	Major histocompatibility complex class I-related gene protein	protein	248	29% helix, 41% strand	Q95460
D	TCR alpha chain	protein	200	4% helix, 46% strand	—
E	TCR beta chain	protein	243	7% helix, 49% strand	—
F	Beta-2-microglobulin	protein	97	0% helix, 51% strand	P61769
G	TCR alpha chain	protein	190	3% helix, 48% strand	—
H	TCR beta chain	protein	242	6% helix, 50% strand	—

Ligands and binding sites

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

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

Pockets

14 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	425	0.76	0.85	61	2LJ
2	401	0.75	0.85	59	2LJ
3	1019	0.72	0.76	83	empty
4	991	0.72	0.76	79	empty
5	469	0.71	0.81	37	empty

Interfaces

11 interfaces between chains.

D–E · 1985 Å² buried · 17 hydrogen bonds · protein-protein
G–H · 1953 Å² buried · 25 hydrogen bonds · protein-protein
C–F · 1194 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 1191 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 668 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

4NQD · Crystal structure of TCR-MR1 ternary complex and non-covalently bound… · the same entry in another collection · chain H against H, 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 4NQD · PDBe 4NQD · UniProt Q95460 · UniProt P61769

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