Research workbench
Cryo-EM structure of a human TRPM4 channel in complex with calcium and decavanadate
Analyse Cryo-EM structure of a human TRPM4 channel in complex with calcium and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WP6
- Type
- protein
- Length
- 3,908 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
- DVT
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 1 distinct chain · 55% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Transient receptor potential cation channel subfamily M member 4 | protein | 977 | 55% helix, 6% strand | Q8TD43 |
Ligands and binding sites
- DVT · Decavanadate · ligand · 8 copies · chains A, D, B, C
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 | 730 | 0.86 | 0.89 | 52 | empty |
| 2 | 1028 | 0.82 | 0.83 | 119 | empty |
| 3 | 1190 | 0.81 | 0.82 | 102 | empty |
| 4 | 1168 | 0.80 | 0.81 | 93 | empty |
| 5 | 890 | 0.80 | 0.82 | 94 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3762 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 3751 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 3742 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 3737 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 59 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5WP6 · Cryo-EM structure of a human TRPM4 channel in complex with calcium and decavanadate · 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 0.80
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 5WP6 · PDBe 5WP6 · UniProt Q8TD43
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