Research workbench
Cryo-EM structure of the zebrafish TRPM2 channel in the presence of CA2+
Analyse Cryo-EM structure of the zebrafish TRPM2 channel in the presence of CA2+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D73
- Type
- protein
- Length
- 4,966 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transient receptor potential cation channel, subfamily M
- Ligands
- CA
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 53% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D | Transient receptor potential cation channel, subfamily M | protein | 1256 | 53% helix, 8% strand | — |
| A, C | Transient receptor potential cation channel, subfamily M | protein | 1227 | 53% helix, 9% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains B, A, 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 | 824 | 0.83 | 0.86 | 78 | empty |
| 2 | 1101 | 0.83 | 0.84 | 86 | empty |
| 3 | 435 | 0.80 | 0.88 | 62 | empty |
| 4 | 942 | 0.79 | 0.81 | 85 | CA |
| 5 | 466 | 0.79 | 0.86 | 64 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3111 Ų buried · 13 hydrogen bonds · protein-protein
- B–A · 3097 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 2932 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 2797 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 96 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6D73 · Cryo-EM structure of the zebrafish TRPM2 channel in the presence of Ca2+ · the same entry in another collection · chain B against B, 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 6D73 · PDBe 6D73
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