MolNFT v1 · #162294 · protein
Crystal structure of S. cerevisia niemann-pick type C protein NPC2
6R4M · PHOSPHATIDYLGLYCEROL/PHOSPHATIDYLINOSITOL transfer protein: “Crystal structure of S. cerevisia niemann-pick type C protein NPC2”. X-ray diffraction, 1 ligand (NAG), 8 pockets (best druggability 0.80). MolNFT v1 #162294 on GenesisL1…
- PDB
- 6R4M
- Type
- protein
- Length
- 435 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PHOSPHATIDYLGLYCEROL/PHOSPHATIDYLINOSITOL transfer protein
- UniProt
- Q12408
- Ligands
- NAG
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PHOSPHATIDYLGLYCEROL/PHOSPHATIDYLINOSITOL transfer protein | protein | 142 | 5% helix, 54% strand | Q12408 |
| B | PHOSPHATIDYLGLYCEROL/PHOSPHATIDYLINOSITOL transfer protein | protein | 143 | 5% helix, 52% strand | Q12408 |
| C | PHOSPHATIDYLGLYCEROL/PHOSPHATIDYLINOSITOL transfer protein | protein | 150 | 5% helix, 51% strand | Q12408 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 973 | 0.80 | 0.81 | 56 | empty |
| 2 | 985 | 0.80 | 0.81 | 56 | empty |
| 3 | 1044 | 0.79 | 0.80 | 58 | empty |
| 4 | 140 | 0.51 | 0.79 | 33 | empty |
| 5 | 118 | 0.43 | 0.77 | 18 | empty |
Interfaces
3 interfaces between chains.
- B–C · 567 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 531 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 531 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6R4M · Crystal structure of S. cerevisia Niemann-Pick type C protein NPC2 · the same entry in another collection · chain A against A, 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 0.98
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 6R4M · PDBe 6R4M · UniProt Q12408
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