Research workbench
Human TRPM4 ion channel in lipid nanodiscs in a calcium-bound state
Analyse Human TRPM4 ion channel in lipid nanodiscs in a calcium-bound state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BQV
- Type
- protein
- Length
- 3,728 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transient receptor potential cation channel subfamily M member 4
- UniProt
- Q8TD43
- Ligands
- Y01, CA
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 58% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Transient receptor potential cation channel subfamily M member 4 | protein | 932 | 58% helix, 5% strand | Q8TD43 |
Ligands and binding sites
- Y01 · Cholesterol hemisuccinate · ligand · 12 copies · chains A, C, B, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1117 | 0.84 | 0.85 | 103 | empty |
| 2 | 1022 | 0.79 | 0.80 | 89 | empty |
| 3 | 1036 | 0.78 | 0.80 | 90 | empty |
| 4 | 1036 | 0.78 | 0.80 | 88 | empty |
| 5 | 1029 | 0.78 | 0.80 | 83 | empty |
Interfaces
6 interfaces between chains.
- B–D · 3653 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 3635 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 3628 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 3625 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 62 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6BQV · Human TRPM4 ion channel in lipid nanodiscs in a calcium-bound state · the same entry in another collection · chain A against A, TM-score 1.00
- Q8TD43 · AlphaFold monomer V2.0 prediction for transient receptor potential cation channel… · a predicted model of the same protein · chain A against A, TM-score 0.85
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 Q8TD43
- Elsewhere: RCSB PDB 6BQV · PDBe 6BQV · UniProt Q8TD43
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