Research workbench
Supernatant protein factor in complex with rrr-alpha-tocopherylquinone: a link between oxidized vitamin E and cholesterol biosynthesis
Analyse Supernatant protein factor in complex with rrr-alpha-tocopherylquinone: a link… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OLM
- Type
- protein
- Length
- 1,174 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SEC14-like protein 2
- UniProt
- O76054
- Ligands
- VTQ
- Pockets
- 19 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SEC14-like protein 2 | protein | 393 | 39% helix, 24% strand | O76054 |
| C | SEC14-like protein 2 | protein | 384 | 39% helix, 25% strand | O76054 |
| E | SEC14-like protein 2 | protein | 397 | 38% helix, 25% strand | O76054 |
Ligands and binding sites
- VTQ · Rrr-alpha-tocopherylquinone · ligand · 3 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 410 | 0.87 | 0.94 | 50 | VTQ |
| 2 | 416 | 0.87 | 0.94 | 50 | VTQ |
| 3 | 417 | 0.87 | 0.94 | 51 | VTQ |
| 4 | 1116 | 0.86 | 0.87 | 113 | empty |
| 5 | 814 | 0.72 | 0.77 | 61 | empty |
Interfaces
3 interfaces between chains.
- A–E · 700 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 598 Ų buried · 11 hydrogen bonds · protein-protein
- C–E · 597 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1OLM · Supernatant Protein Factor in Complex with RRR-alpha-Tocopherylqui : A Link between… · the same entry in another collection · chain A against A, TM-score 1.00
- O76054 · AlphaFold monomer V2.0 prediction for SEC14-like protein 2 (O76054) · a predicted model of the same protein · chain E against A, TM-score 0.99
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 O76054
- Elsewhere: RCSB PDB 1OLM · PDBe 1OLM · UniProt O76054
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