MolNFT v1 · #181137 · protein

Stimulatory immune receptor protein complex

7LLI · Major histocompatibility complex class I-related gene…: “Stimulatory immune receptor protein complex”. X-ray diffraction, 1 ligand (2LJ), 20 pockets (best druggability 0.76). MolNFT v1 #181137 on GenesisL1: 3D structure, binding…

PDB: 7LLI
Type: protein
Length: 1,619 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; T…
UniProt: Q95460, P61769, A0A0C4DH27, A0JD37
Ligands: 2LJ
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 5 distinct chains · 10% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, A	Major histocompatibility complex class I-related gene protein	protein	263	29% helix, 37% strand	Q95460
D, B	Beta-2-microglobulin	protein	98	0% helix, 48% strand	P61769
K, E	T cell receptor gamma variable 8	protein	237	6% helix, 46% strand	A0A0C4DH27
L	T cell receptor delta variable 3	protein	212	4% helix, 42% strand	A0JD37
F	T cell receptor delta variable 3	protein	211	3% helix, 43% strand	A0JD37

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 C, A

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

Pockets

20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	773	0.76	0.80	84	2LJ
2	942	0.75	0.78	72	empty
3	936	0.74	0.78	85	empty
4	714	0.73	0.79	73	2LJ
5	519	0.64	0.76	50	empty

Interfaces

11 interfaces between chains.

K–L · 2423 Å² buried · 27 hydrogen bonds · protein-protein
E–F · 2370 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1247 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 1169 Å² buried · 10 hydrogen bonds · protein-protein
C–L · 802 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

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

Compared structures

7LLI · Stimulatory immune receptor protein complex · the same entry in another collection · chain F against F, 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 0.97
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 0.94

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
Every structure of UniProt A0A0C4DH27
Every structure of UniProt A0JD37
Elsewhere: RCSB PDB 7LLI · PDBe 7LLI · UniProt Q95460 · UniProt P61769 · UniProt A0A0C4DH27 · UniProt A0JD37

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