Research workbench
Crystal structure of the lysosomal potassium channel MTTMEM175 T38A mutant soaked with zinc
Analyse Crystal structure of the lysosomal potassium channel MTTMEM175 T38A mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SWR
- Type
- protein
- Length
- 1,372 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nanobody, MALTOSE/MALTODEXTRIN-binding periplasmic protein, maltodextrin-binding…
- UniProt
- P0AEX9, E4TN31
- Ligands
- GLC, K
- Pockets
- 19 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Nanobody, MALTOSE/MALTODEXTRIN-binding periplasmic protein, maltodextrin-binding PROTEIN,MALTOSE/MALTODEXTRIN-binding periplasmic protein | protein | 460 | 38% helix, 27% strand | P0AEX9 |
| B | Uncharacterized protein | protein | 230 | 77% helix, 0% strand | E4TN31 |
| E | Uncharacterized protein | protein | 222 | 74% helix, 0% strand | E4TN31 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, D
- K · Potassium ion · metal
- LMT · Dodecyl-beta-D-maltoside · additive · 2 copies · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 308 | 0.73 | 0.85 | 36 | GLC |
| 2 | 271 | 0.72 | 0.86 | 31 | GLC |
| 3 | 613 | 0.71 | 0.78 | 55 | empty |
| 4 | 536 | 0.68 | 0.77 | 40 | empty |
| 5 | 303 | 0.53 | 0.74 | 29 | empty |
Interfaces
5 interfaces between chains.
- B–E · 1776 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 529 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 520 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 97 Ų buried · 1 hydrogen bond · protein-protein
- A–E · 59 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6SWR · Crystal structure of the lysosomal potassium channel MtTMEM175 T38A mutant soaked with… · the same entry in another collection · chain A against A, TM-score 1.00
- E4TN31 · AlphaFold monomer V2.0 prediction for potassium channel FTRAC_2467 (E4TN31) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 P0AEX9
- Every structure of UniProt E4TN31
- Elsewhere: RCSB PDB 6SWR · PDBe 6SWR · UniProt P0AEX9 · UniProt E4TN31
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