MolNFT v1 · #91240 · protein
Structure of the lysosomal domain of limp-2
4F7B · Lysosome membrane protein 2: “Structure of the lysosomal domain of limp-2”. X-ray diffraction, 4 ligands (NAG, BMA, MAN), 20 pockets (best druggability 0.86). MolNFT v1 #91240 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4F7B
- Type
- protein
- Length
- 2,333 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysosome membrane protein 2
- UniProt
- Q14108
- Ligands
- NAG, BMA, MAN, PO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 6 distinct chains · 23% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysosome membrane protein 2 | protein | 393 | 25% helix, 33% strand | Q14108 |
| B | Lysosome membrane protein 2 | protein | 393 | 23% helix, 34% strand | Q14108 |
| C | Lysosome membrane protein 2 | protein | 378 | 22% helix, 34% strand | Q14108 |
| D | Lysosome membrane protein 2 | protein | 389 | 24% helix, 34% strand | Q14108 |
| E | Lysosome membrane protein 2 | protein | 390 | 23% helix, 34% strand | Q14108 |
| F | Lysosome membrane protein 2 | protein | 390 | 24% helix, 34% strand | Q14108 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 73 copies · chains A, B, C, D, E, F
- BMA · beta-D-mannopyranose · sugar · 17 copies · chains B, D, E
- MAN · alpha-D-mannopyranose · sugar · 12 copies · chains A, B, D, E, F
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, C, D, E, F
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, F
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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 814 | 0.86 | 0.88 | 70 | empty |
| 2 | 1060 | 0.86 | 0.86 | 96 | PO4, PEG |
| 3 | 1101 | 0.86 | 0.86 | 98 | PO4 |
| 4 | 1160 | 0.86 | 0.86 | 103 | PO4 |
| 5 | 1139 | 0.85 | 0.86 | 114 | PO4, PEG |
Interfaces
5 interfaces between chains.
- B–E · 711 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 711 Ų buried · 1 hydrogen bond · protein-protein
- D–F · 353 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 199 Ų buried · 0 hydrogen bonds · protein-protein
- A–F · 120 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 42 glycan, 12 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 4F7B · PDBe 4F7B · UniProt Q14108
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