MolNFT v1 · #121186 · protein
Structure of glycosylated NPC1 luminal domain C
5HNS · Niemann-pick C1 protein: “Structure of glycosylated NPC1 luminal domain C”. X-ray diffraction, 4 ligands (NAG, BMA, MAN), 5 pockets (best druggability 0.75). MolNFT v1 #121186 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5HNS
- Type
- protein
- Length
- 431 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Niemann-pick C1 protein
- UniProt
- O15118
- Ligands
- NAG, BMA, MAN, SCN
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Niemann-pick C1 protein | protein | 215 | 31% helix, 21% strand | O15118 |
| B | Niemann-pick C1 protein | protein | 216 | 33% helix, 21% strand | O15118 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 17 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains B
- SCN · Thiocyanate ion · ion · 4 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 | 64 | 0.75 | 0.98 | 22 | empty |
| 2 | 363 | 0.64 | 0.79 | 44 | SCN |
| 3 | 312 | 0.60 | 0.78 | 33 | SCN |
| 4 | 112 | 0.41 | 0.76 | 28 | empty |
| 5 | 50 | 0.35 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1422 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 glycan, 4 disulfide (N-glycosylation, disulfide).
Compared structures
- 5HNS · Structure of glycosylated NPC1 luminal domain C · the same entry in another collection · chain A against A, TM-score 1.00
- O15118 · AlphaFold monomer V2.0 prediction for npc intracellular cholesterol transporter 1 (O15118) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 O15118
- Elsewhere: RCSB PDB 5HNS · PDBe 5HNS · UniProt O15118
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