MolNFT v1 · #123553 · protein
The 6.6 a cryo-EM structure of the full-length human NPC1 in complex with the cleaved glycoprotein of ebola virus
5JNX · Niemann-pick C1 protein: “The 6.6 a cryo-EM structure of the full-length human NPC1 in complex with the cleaved glycoprotein of ebola…”. Electron microscopy, 3 ligands (NAG, BMA, MAN), 20 pockets (best druggability 0.88). MolNFT v1…
- PDB
- 5JNX
- Type
- protein
- Length
- 1,868 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Niemann-pick C1 protein; Envelope glycoprotein
- UniProt
- O15118, P87666
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 3 distinct chains · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Niemann-pick C1 protein | protein | 1133 | 51% helix, 9% strand | O15118 |
| C, E, G | Envelope glycoprotein | protein | 158 | 6% helix, 42% strand | P87666 |
| D, F, H | Envelope glycoprotein | protein | 87 | 45% helix, 16% strand | P87666 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 27 copies · chains A, C, D, H, E, F, G
- 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
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1138 | 0.88 | 0.89 | 114 | empty |
| 2 | 883 | 0.83 | 0.84 | 85 | empty |
| 3 | 207 | 0.80 | 0.94 | 43 | empty |
| 4 | 1045 | 0.78 | 0.80 | 88 | empty |
| 5 | 484 | 0.77 | 0.85 | 76 | empty |
Interfaces
16 interfaces between chains.
- E–F · 2226 Ų buried · 27 hydrogen bonds · protein-protein
- G–H · 2226 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 2223 Ų buried · 27 hydrogen bonds · protein-protein
- D–H · 736 Ų buried · 1 hydrogen bond · protein-protein
- F–H · 736 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 20 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 5JNX · The 6.6 A cryo-EM structure of the full-length human NPC1 in complex with the cleaved… · the same entry in another collection · chain H against H, 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
- Every structure of UniProt P87666
- Elsewhere: RCSB PDB 5JNX · PDBe 5JNX · UniProt O15118 · UniProt P87666
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