Research workbench
Lipids bound lysosomal integral membrane protein 2
Analyse Lipids bound lysosomal integral membrane protein 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UPH
- Type
- protein
- Length
- 640 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysosome membrane protein 2
- UniProt
- Q14108
- Ligands
- PCW, CLR, M6D, NAG, MAN, BMA
- Pockets
- 5 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysosome membrane protein 2 | protein | 316 | 22% helix, 35% strand | Q14108 |
| B | Lysosome membrane protein 2 | protein | 324 | 20% helix, 35% strand | Q14108 |
Ligands and binding sites
- PCW · 1,2-dioleoyl-sn-glycero-3-phosphocholine · ligand · 3 copies · chains A, B
- CLR · Cholesterol · ligand · 2 copies · chains A, B
- M6D · 6-O-phosphono-beta-D-mannopyranose · ligand · chains B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 11 copies · chains B, A
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1025 | 0.86 | 0.87 | 83 | CLR, PCW |
| 2 | 1155 | 0.85 | 0.86 | 96 | CLR, PCW |
| 3 | 112 | 0.54 | 0.82 | 15 | empty |
| 4 | 66 | 0.45 | 0.82 | 17 | empty |
| 5 | 114 | 0.38 | 0.73 | 16 | PCW |
Interfaces
1 interface between chains.
- A–B · 835 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
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 5UPH · PDBe 5UPH · UniProt Q14108
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