MolNFT v1 · #140546 · protein
Structure of endo-lysosomal TRPML1 channel inserting into nanodisc
5YE5 · Mammalian endo-lysosomal TRPML1 channel: “Structure of endo-lysosomal TRPML1 channel inserting into nanodisc”. Electron microscopy, 1 ligand (NAG), 16 pockets (best druggability 0.66). MolNFT v1 #140546 on GenesisL1: 3D structure…
- PDB
- 5YE5
- Type
- protein
- Length
- 1,856 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mammalian endo-lysosomal TRPML1 channel
- UniProt
- Q99J21
- Ligands
- NAG
- Pockets
- 16 · best druggability 0.66
Structure
electron microscopy · 1 distinct chain · 59% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Mammalian endo-lysosomal TRPML1 channel | protein | 464 | 59% helix, 16% strand | Q99J21 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1031 | 0.66 | 0.73 | 130 | empty |
| 2 | 501 | 0.61 | 0.76 | 84 | empty |
| 3 | 509 | 0.61 | 0.75 | 79 | empty |
| 4 | 286 | 0.52 | 0.75 | 44 | empty |
| 5 | 224 | 0.51 | 0.77 | 45 | empty |
Interfaces
4 interfaces between chains.
- B–C · 456 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 455 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 450 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 448 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 glycan (N-glycosylation).
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 Q99J21
- Elsewhere: RCSB PDB 5YE5 · PDBe 5YE5 · UniProt Q99J21
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