Research workbench
The structure of mouse AsterA (GramD1a) with 25-hydroxy cholesterol
Analyse The structure of mouse AsterA (GramD1a) with 25-hydroxy cholesterol in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GQF
- Type
- protein
- Length
- 666 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.9
- Source
- Mus musculus
- Molecule
- GRAM domain-containing protein 1A
- UniProt
- Q8VEF1
- Ligands
- HC3
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · resolution 2.9 · 4 distinct chains · 27% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GRAM domain-containing protein 1A | protein | 168 | 26% helix, 42% strand | Q8VEF1 |
| B | GRAM domain-containing protein 1A | protein | 163 | 25% helix, 42% strand | Q8VEF1 |
| C | GRAM domain-containing protein 1A | protein | 168 | 30% helix, 40% strand | Q8VEF1 |
| D | GRAM domain-containing protein 1A | protein | 167 | 29% helix, 44% strand | Q8VEF1 |
Ligands and binding sites
- HC3 · 25-hydroxycholesterol · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 418 | 0.81 | 0.89 | 45 | HC3, GOL |
| 2 | 1031 | 0.80 | 0.82 | 91 | empty |
| 3 | 411 | 0.79 | 0.87 | 41 | HC3 |
| 4 | 439 | 0.76 | 0.84 | 46 | HC3, GOL |
| 5 | 698 | 0.75 | 0.81 | 75 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1073 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 737 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 692 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 255 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 208 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
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 Q8VEF1
- Elsewhere: RCSB PDB 6GQF · PDBe 6GQF · UniProt Q8VEF1
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