MolNFT v1 · #158473 · protein

CD1A-lipid binary complex

6NUX · CD1A protein: “CD1A-lipid binary complex”. X-ray diffraction, 1 ligand (FOF), 4 pockets (best druggability 0.85). MolNFT v1 #158473 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6NUX
Type: protein
Length: 374 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CD1A protein; Beta-2-microglobulin
UniProt: Q8N5T0, P61769
Ligands: FOF
Pockets: 4 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 19% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	CD1A protein	protein	270	27% helix, 40% strand	Q8N5T0
B	Beta-2-microglobulin	protein	104	0% helix, 47% strand	P61769

Ligands and binding sites

FOF · (2E,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-ol · ligand · chains A
EDO · 1,2-ethanediol · additive · 3 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	741	0.85	0.88	48	FOF
2	348	0.61	0.78	40	EDO
3	112	0.41	0.77	25	EDO
4	80	0.38	0.77	20	empty

Interfaces

1 interface between chains.

A–B · 1406 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

6NUX · CD1a-lipid binary complex · the same entry in another collection · chain A against A, 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 0.91

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 Q8N5T0
Every structure of UniProt P61769
Elsewhere: RCSB PDB 6NUX · PDBe 6NUX · UniProt Q8N5T0 · UniProt P61769

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