MolNFT v1 · #164406 · protein
Crystal structure of the lysosomal potassium channel MTTMEM175 T38A mutant soaked with zinc
6SWR · Nanobody, MALTOSE/MALTODEXTRIN-binding periplasmic protein…: “Crystal structure of the lysosomal potassium channel MTTMEM175 T38A mutant soaked with zinc”. X-ray diffraction, 2 ligands (GLC, K), 19 pockets (best druggability 0.73).…
- 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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