MolNFT v1 · #139302 · protein

Structure of SCARB2-JL2 complex

5XBM · Light chain of JL2: “Structure of SCARB2-JL2 complex”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 19 pockets (best druggability 0.84). MolNFT v1 #139302 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5XBM
Type: protein
Length: 1,646 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Light chain of JL2; Heavy chain of JL2; Lysosome membrane protein 2
UniProt: Q14108
Ligands: NAG, MAN, BMA
Pockets: 19 · best druggability 0.84

Structure

x-ray diffraction · 4 distinct chains · 12% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Light chain of JL2	protein	209	5% helix, 38% strand	—
B, E	Heavy chain of JL2	protein	221	4% helix, 42% strand	—
C	Lysosome membrane protein 2	protein	394	17% helix, 30% strand	Q14108
F	Lysosome membrane protein 2	protein	392	16% helix, 31% strand	Q14108

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 26 copies · chains C, F
MAN · alpha-D-mannopyranose · sugar · 9 copies · chains C, F
BMA · beta-D-mannopyranose · sugar · 6 copies · chains C, F

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

Pockets

19 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	1025	0.84	0.85	105	empty
2	1021	0.84	0.85	106	empty
3	629	0.64	0.75	55	empty
4	482	0.60	0.75	54	empty
5	484	0.58	0.74	48	empty

Interfaces

9 interfaces between chains.

A–B · 1925 Å² buried · 17 hydrogen bonds · protein-protein
D–E · 1906 Å² buried · 14 hydrogen bonds · protein-protein
E–F · 700 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 680 Å² buried · 8 hydrogen bonds · protein-protein
C–F · 475 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 glycan, 10 disulfide (N-glycosylation, disulfide).

Compared structures

5XBM · Structure of SCARB2-JL2 complex · the same entry in another collection · chain F against F, TM-score 1.00
Q14108 · AlphaFold monomer V2.0 prediction for lysosome membrane protein 2 (Q14108) · a predicted model of the same protein · chain F against A, TM-score 0.99

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 Q14108
Elsewhere: RCSB PDB 5XBM · PDBe 5XBM · UniProt Q14108

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.