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Structure of endo-lysosomal TRPML1 channel inserting into amphipol: state 1
Analyse Structure of endo-lysosomal TRPML1 channel inserting into amphipol: state 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YDZ
- Type
- protein
- Length
- 1,696 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mammalian endo-lysosomal TRPML1 channel
- UniProt
- Q99J21
- Pockets
- 17 · best druggability 0.67
Structure
electron microscopy · 1 distinct chain · 59% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Mammalian endo-lysosomal TRPML1 channel | protein | 424 | 59% helix, 14% strand | Q99J21 |
Pockets
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 964 | 0.67 | 0.74 | 104 | empty |
| 2 | 536 | 0.62 | 0.76 | 83 | empty |
| 3 | 491 | 0.61 | 0.76 | 81 | empty |
| 4 | 325 | 0.54 | 0.75 | 60 | empty |
| 5 | 228 | 0.51 | 0.77 | 35 | empty |
Interfaces
4 interfaces between chains.
- A–B · 409 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 403 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 401 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 399 Ų buried · 1 hydrogen bond · protein-protein
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 5YDZ · PDBe 5YDZ · UniProt Q99J21
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