Research workbench
Cryo-EM structure of mouse TEMSIROLIMUS/PI(3,5)P2-bound TRPML1 channel at 2.11 ångström resolution
Analyse Cryo-EM structure of mouse TEMSIROLIMUS/PI(3,5)P2-bound TRPML1 channel at 2.11… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SQ9
- Type
- protein
- Length
- 1,876 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mucolipin-1
- UniProt
- Q99J21
- Ligands
- EUJ, A4I, NAG, NA
- Pockets
- 20 · best druggability 0.83
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 | 469 | 61% helix, 15% strand | Q99J21 |
Ligands and binding sites
- EUJ · (2R)-3-{[(S)-hydroxy{[(1s,2r,3r,4s,5s,6r)-2,4,6-trihydroxy-3,5-bis(phosphonooxy) cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dioctanoate · ligand · 4 copies · chains A, B, C, D
- A4I · (1R,2R,4S)-4-{(2R)-2-[(3S,6R,7E,9R,10R,12R,14S,15E,17E, 19e,21s,23s,26r,27r,30s,34as)-9,27-dihydroxy-10,21-dimethoxy-6,8,12,14,20,26-hexamethyl-1,5,11,28,29-pentaoxo-1,4,5,6,9,10,11,12,13,14,21,22,23,24,25,26, 27,28,29,31,32,33,34,34A-tetracosahydro-3H-23,27-epoxypyrido[2,1-c][1,4]oxazacyclohentriacontin-3-yl]propyl}-2-methoxycyclohexyl 3-hydroxy-2-(hydroxymethyl)-2-methylpropanoate · ligand · 4 copies · chains A, C, B, D
- 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1098 | 0.83 | 0.84 | 68 | NA |
| 2 | 292 | 0.64 | 0.81 | 33 | EUJ |
| 3 | 292 | 0.63 | 0.80 | 32 | EUJ |
| 4 | 309 | 0.62 | 0.79 | 32 | EUJ |
| 5 | 315 | 0.62 | 0.79 | 34 | EUJ |
Interfaces
4 interfaces between chains.
- B–C · 3612 Ų buried · 37 hydrogen bonds · protein-protein
- B–D · 3598 Ų buried · 37 hydrogen bonds · protein-protein
- A–D · 3598 Ų buried · 37 hydrogen bonds · protein-protein
- A–C · 3595 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan (N-glycosylation).
Compared structures
- 7SQ9 · Cryo-EM structure of mouse temsirolimus/PI(3,5)P2-bound TRPML1 channel at 2.11 Angstrom… · 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 7SQ9 · PDBe 7SQ9 · UniProt Q99J21
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