Research workbench
Cryo-EM structure of mammalian endolysosomal TRPML1 channel in nanodiscs in closed I conformation at 3.64 ångström resolution
Analyse Cryo-EM structure of mammalian endolysosomal TRPML1 channel in nanodiscs in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WPQ
- Type
- protein
- Length
- 1,816 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mucolipin-1
- UniProt
- Q99J21
- Ligands
- NAG, NA
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 57% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Mucolipin-1 | protein | 454 | 57% helix, 13% strand | Q99J21 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
- NA · Sodium ion · metal
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 775 | 0.84 | 0.86 | 87 | empty |
| 2 | 857 | 0.73 | 0.77 | 58 | empty |
| 3 | 707 | 0.72 | 0.78 | 62 | empty |
| 4 | 645 | 0.71 | 0.79 | 48 | empty |
| 5 | 638 | 0.71 | 0.78 | 49 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3561 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 3556 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 3549 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 3543 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 17 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan (N-glycosylation).
Compared structures
- 5WPQ · Cryo-EM structure of mammalian endolysosomal TRPML1 channel in nanodiscs in closed I… · 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 5WPQ · PDBe 5WPQ · UniProt Q99J21
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