Research workbench
Cryo-EM structure of mouse agonist ml-SA1-bound TRPML1 channel at 2.32 ångström resolution
Analyse Cryo-EM structure of mouse agonist ml-SA1-bound TRPML1 channel at 2.32 ångström… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SQ6
- Type
- protein
- Length
- 1,868 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mucolipin-1
- UniProt
- Q99J21
- Ligands
- AQV, NAG, NA
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 1 distinct chain · 61% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Mucolipin-1 | protein | 467 | 61% helix, 15% strand | Q99J21 |
Ligands and binding sites
- AQV · 2-{2-oxo-2-[(4S)-2,2,4-trimethyl-3,4-dihydroquinolin-1(2H)-yl]ethyl}-1H-isoindole-1,3(2H)-dione · ligand · 4 copies · chains A, D, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
- NA · Sodium ion · metal · 2 copies · chains A, B, C, D
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 | 1057 | 0.85 | 0.86 | 58 | NA |
| 2 | 626 | 0.71 | 0.78 | 72 | AQV |
| 3 | 430 | 0.66 | 0.78 | 62 | empty |
| 4 | 441 | 0.63 | 0.76 | 42 | AQV |
| 5 | 232 | 0.62 | 0.81 | 41 | empty |
Interfaces
4 interfaces between chains.
- B–C · 3587 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 3580 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 3573 Ų buried · 33 hydrogen bonds · protein-protein
- A–D · 3572 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan (N-glycosylation).
Compared structures
- 7SQ6 · Cryo-EM structure of mouse agonist ML-SA1-bound TRPML1 channel at 2.32 Angstrom resolution · the same entry in another collection · chain A against A, TM-score 1.00
- Q99J21 · AlphaFold monomer V2.0 prediction for mucolipin-1 (Q99J21) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q99J21
- Elsewhere: RCSB PDB 7SQ6 · PDBe 7SQ6 · UniProt Q99J21
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