MolNFT v1 · #103526 · protein

Structure of human MR1-5-op-ru in complex with human mait C-C10 TCR

4PJD · Major histocompatibility complex class I-related gene…: “Structure of human MR1-5-op-ru in complex with human mait C-C10 TCR”. X-ray diffraction, 1 ligand (2LJ), 15 pockets (best druggability 0.76). MolNFT v1 #103526 on GenesisL1…

PDB: 4PJD
Type: protein
Length: 1,567 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: 2LJ
Pockets: 15 · best druggability 0.76

Structure

x-ray diffraction · 7 distinct chains · 13% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Major histocompatibility complex class I-related gene protein	protein	264	27% helix, 41% strand	Q95460
B, D	Beta-2-microglobulin	protein	96	0% helix, 51% strand	P61769
C	Major histocompatibility complex class I-related gene protein	protein	254	28% helix, 40% strand	Q95460
E	TCR-alpha	protein	188	5% helix, 47% strand	—
F	TCR-beta	protein	233	6% helix, 48% strand	—
G	TCR-alpha	protein	197	5% helix, 46% strand	—
H	TCR-beta	protein	239	6% helix, 49% 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, E, F, C, G, H
GOL · Glycerol · additive · chains E

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

Pockets

15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	417	0.76	0.85	54	2LJ
2	852	0.76	0.79	77	empty
3	381	0.75	0.85	45	2LJ
4	168	0.71	0.89	36	empty
5	1014	0.71	0.75	80	empty

Interfaces

11 interfaces between chains.

G–H · 1915 Å² buried · 17 hydrogen bonds · protein-protein
E–F · 1739 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 1166 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 1160 Å² buried · 17 hydrogen bonds · protein-protein
C–G · 702 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

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

Compared structures

4PJD · Structure of human MR1-5-OP-RU in complex with human MAIT C-C10 TCR · 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 D 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 4PJD · PDBe 4PJD · UniProt Q95460 · UniProt P61769

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