Research workbench
Crystal structure of the potassium channel MtTMEM175 in complex with a Nanobody-MBP fusion protein
Analyse Crystal structure of the potassium channel MtTMEM175 in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HD8
- Type
- protein
- Length
- 693 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.4
- Source
- Escherichia coli (strain K12); Lama glama; Marivirga tractuosa DSM 4126
- Molecule
- Nanobody,Maltose/maltodextrin-binding periplasmic protein; TMEM175
- UniProt
- P0AEX9, E4TN31
- Ligands
- GLC, K
- Pockets
- 10 · best druggability 0.73
Structure
x-ray diffraction · resolution 2.4 · 2 distinct chains · 51% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nanobody,Maltose/maltodextrin-binding periplasmic protein | protein | 461 | 38% helix, 27% strand | P0AEX9 |
| B | TMEM175 | protein | 232 | 77% helix, 0% strand | E4TN31 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A
- K · Potassium ion · metal · 2 copies · chains B
- LMT · Dodecyl-beta-D-maltoside · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 283 | 0.73 | 0.86 | 32 | GLC |
| 2 | 466 | 0.68 | 0.78 | 39 | empty |
| 3 | 110 | 0.49 | 0.80 | 18 | empty |
| 4 | 66 | 0.46 | 0.83 | 20 | empty |
| 5 | 92 | 0.36 | 0.75 | 15 | LMT |
Interfaces
1 interface between chains.
- A–B · 547 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6HD8 · Crystal structure of the potassium channel MTTMEM175 in complex with a nanobody-mbp… · 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 0.89
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 6HD8 · PDBe 6HD8 · UniProt P0AEX9 · UniProt E4TN31
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