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Crystal structure of S. cerevisia niemann-pick type C protein NPC2 with ergosterol bound
Analyse Crystal structure of S. cerevisia niemann-pick type C protein NPC2 with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6R4N
- Type
- protein
- Length
- 1,296 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PHOSPHATIDYLGLYCEROL/PHOSPHATIDYLINOSITOL transfer protein
- UniProt
- Q12408
- Ligands
- ERG, NAG, SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 7 distinct chains · 5% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G, I | PHOSPHATIDYLGLYCEROL/PHOSPHATIDYLINOSITOL transfer protein | protein | 144 | 5% helix, 53% strand | Q12408 |
| B | PHOSPHATIDYLGLYCEROL/PHOSPHATIDYLINOSITOL transfer protein | protein | 141 | 5% helix, 52% strand | Q12408 |
| C | PHOSPHATIDYLGLYCEROL/PHOSPHATIDYLINOSITOL transfer protein | protein | 147 | 5% helix, 52% strand | Q12408 |
| D | PHOSPHATIDYLGLYCEROL/PHOSPHATIDYLINOSITOL transfer protein | protein | 142 | 5% helix, 51% strand | Q12408 |
| E | PHOSPHATIDYLGLYCEROL/PHOSPHATIDYLINOSITOL transfer protein | protein | 143 | 5% helix, 52% strand | Q12408 |
| F | PHOSPHATIDYLGLYCEROL/PHOSPHATIDYLINOSITOL transfer protein | protein | 146 | 5% helix, 51% strand | Q12408 |
| H | PHOSPHATIDYLGLYCEROL/PHOSPHATIDYLINOSITOL transfer protein | protein | 145 | 5% helix, 50% strand | Q12408 |
Ligands and binding sites
- ERG · Ergosterol · ligand · 5 copies · chains A, C, G, E, I
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains I, A, B, C, D, E, F, G, H
- SO4 · Sulfate ion · ion · 16 copies · chains A, B, C, E, F, G, H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1050 | 0.82 | 0.82 | 56 | ERG |
| 2 | 826 | 0.81 | 0.83 | 54 | empty |
| 3 | 1070 | 0.81 | 0.81 | 52 | empty |
| 4 | 1004 | 0.81 | 0.81 | 55 | ERG |
| 5 | 1058 | 0.81 | 0.81 | 61 | ERG |
Interfaces
14 interfaces between chains.
- B–C · 580 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 572 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 561 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 558 Ų buried · 7 hydrogen bonds · protein-protein
- H–I · 556 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 6R4N · Crystal structure of S. cerevisia Niemann-Pick type C protein NPC2 with ergosterol bound · the same entry in another collection · chain I against I, TM-score 1.00
- Q12408 · AlphaFold monomer V2.0 prediction for PHOSPHATIDYLGLYCEROL/PHOSPHATIDYLINOSITOL transfer… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q12408
- Elsewhere: RCSB PDB 6R4N · PDBe 6R4N · UniProt Q12408
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