Research workbench
Cryo-EM structure of the zebrafish TRPM2 channel in the apo conformation, processed with C4 symmetry
Analyse Cryo-EM structure of the zebrafish TRPM2 channel in the apo conformation… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PKV
- Type
- protein
- Length
- 4,348 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transient receptor potential cation channel subfamily M member 2
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 1 distinct chain · 56% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Transient receptor potential cation channel subfamily M member 2 | protein | 1087 | 56% helix, 8% strand | — |
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 | 1041 | 0.80 | 0.81 | 108 | empty |
| 2 | 1052 | 0.80 | 0.81 | 109 | empty |
| 3 | 975 | 0.79 | 0.81 | 87 | empty |
| 4 | 1083 | 0.79 | 0.80 | 115 | empty |
| 5 | 205 | 0.74 | 0.89 | 36 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1246 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 1232 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 1217 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 1215 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 22 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6PKV · Cryo-EM structure of the zebrafish TRPM2 channel in the apo conformation, processed with… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 6PKV · PDBe 6PKV
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