Research workbench
Cryo-EM structure of TRPV5 with calmodulin bound
Analyse Cryo-EM structure of TRPV5 with calmodulin bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6O20
- Type
- protein
- Length
- 2,624 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transient receptor potential cation channel subfamily V member 5; Calmodulin
- UniProt
- Q9XSM3, P62157
- Ligands
- CA
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 4 distinct chains · 52% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transient receptor potential cation channel subfamily V member 5 | protein | 627 | 53% helix, 4% strand | Q9XSM3 |
| E | Transient receptor potential cation channel subfamily V member 5 | protein | 13 | 85% helix, 0% strand | Q9XSM3 |
| F | Calmodulin | protein | 148 | 47% helix, 1% strand | P62157 |
| B, C, D | Transient receptor potential cation channel subfamily V member 5 | protein | 612 | 52% helix, 4% strand | Q9XSM3 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 937 | 0.82 | 0.84 | 111 | empty |
| 2 | 164 | 0.81 | 0.97 | 25 | empty |
| 3 | 364 | 0.78 | 0.87 | 51 | empty |
| 4 | 306 | 0.76 | 0.87 | 45 | empty |
| 5 | 360 | 0.76 | 0.86 | 49 | empty |
Interfaces
11 interfaces between chains.
- A–B · 3633 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 3576 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 3573 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 3559 Ų buried · 25 hydrogen bonds · protein-protein
- A–F · 1839 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6O20 · Cryo-EM structure of TRPV5 with calmodulin bound · the same entry in another collection · chain D against D, TM-score 1.00
- Q9XSM3 · AlphaFold monomer V2.0 prediction for transient receptor potential cation channel… · a predicted model of the same protein · chain B against A, TM-score 0.98
- P62157 · AlphaFold monomer V2.0 prediction for calmodulin (P62157) · a predicted model of the same protein · chain F against A, TM-score 0.49
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 Q9XSM3
- Every structure of UniProt P62157
- Elsewhere: RCSB PDB 6O20 · PDBe 6O20 · UniProt Q9XSM3 · UniProt P62157
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