MolNFT v1 · #151089 · protein
Crystal structure of the potassium channel MTTMEM175 with rubidium
6HD9 · NANOBODY,MALTOSE/MALTODEXTRIN-binding periplasmic protein: “Crystal structure of the potassium channel MTTMEM175 with rubidium”. X-ray diffraction, 2 ligands (GLC, RB), 8 pockets (best druggability 0.74). MolNFT v1 #151089 on…
- PDB
- 6HD9
- Type
- protein
- Length
- 693 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NANOBODY,MALTOSE/MALTODEXTRIN-binding periplasmic protein; TMEM175
- UniProt
- P0AEX9, E4TN31
- Ligands
- GLC, RB
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NANOBODY,MALTOSE/MALTODEXTRIN-binding periplasmic protein | protein | 461 | 37% 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
- RB · Rubidium ion · metal
- LMT · Dodecyl-beta-D-maltoside · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 284 | 0.74 | 0.86 | 30 | GLC |
| 2 | 472 | 0.68 | 0.78 | 41 | empty |
| 3 | 114 | 0.50 | 0.80 | 18 | empty |
| 4 | 58 | 0.46 | 0.84 | 20 | empty |
| 5 | 112 | 0.45 | 0.78 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 535 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6HD9 · Crystal structure of the potassium channel MtTMEM175 with rubidium · 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 6HD9 · PDBe 6HD9 · UniProt P0AEX9 · UniProt E4TN31
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