MolNFT v1 · #68229 · protein
Cryo-EM structure of the full-length human NPC1 at 4.4 ångström
3JD8 · Niemann-pick C1 protein: “Cryo-EM structure of the full-length human NPC1 at 4.4 ångström”. Electron microscopy, 4 ligands (CLR, NAG, BMA), 18 pockets (best druggability 0.84). MolNFT v1 #68229 on GenesisL1: 3D structure, binding…
- PDB
- 3JD8
- Type
- protein
- Length
- 1,133 residues
- Chains
- 1
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Niemann-pick C1 protein
- UniProt
- O15118
- Ligands
- CLR, NAG, BMA, MAN
- Pockets
- 18 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 51% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Niemann-pick C1 protein | protein | 1133 | 51% helix, 9% strand | O15118 |
Ligands and binding sites
- CLR · Cholesterol · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 21 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A
- MAN · alpha-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1126 | 0.84 | 0.84 | 123 | empty |
| 2 | 293 | 0.81 | 0.92 | 57 | empty |
| 3 | 280 | 0.79 | 0.91 | 29 | CLR |
| 4 | 194 | 0.76 | 0.91 | 33 | empty |
| 5 | 840 | 0.74 | 0.78 | 116 | empty |
Modifications
Observed in the structure: 11 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 3JD8 · cryo-EM structure of the full-length human NPC1 at 4.4 angstrom · 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 0.85
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 3JD8 · PDBe 3JD8 · UniProt O15118
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