MolNFT v1 · #104233 · protein
Crystal structure of limp-2 (space group C2221)
4Q4B · Lysosome membrane protein 2: “Crystal structure of limp-2 (space group C2221)”. X-ray diffraction, 4 ligands (NAG, MAN, BMA), 4 pockets (best druggability 0.85). MolNFT v1 #104233 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4Q4B
- Type
- protein
- Length
- 392 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysosome membrane protein 2
- UniProt
- Q14108
- Ligands
- NAG, MAN, BMA, NA
- Pockets
- 4 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysosome membrane protein 2 | protein | 392 | 22% helix, 34% strand | Q14108 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 11 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains A
- NA · Sodium ion · metal · 2 copies · chains A
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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1099 | 0.85 | 0.86 | 99 | empty |
| 2 | 191 | 0.60 | 0.82 | 36 | NAG |
| 3 | 83 | 0.43 | 0.80 | 15 | NAG |
| 4 | 68 | 0.40 | 0.79 | 14 | empty |
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 4Q4B · PDBe 4Q4B · UniProt Q14108
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