Research workbench
Calmodulin-bound full-length rbTRPV5
Analyse Calmodulin-bound full-length rbTRPV5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DMW
- Type
- protein
- Length
- 2,562 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4.4
- Source
- Oryctolagus cuniculus; Rattus norvegicus
- Molecule
- Transient receptor potential cation channel subfamily V member 5; Calmodulin-1
- UniProt
- Q9XSM3, P0DP29
- Ligands
- CA
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · resolution 4.4 · 5 distinct chains · 61% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transient receptor potential cation channel subfamily V member 5 | protein | 631 | 62% helix, 5% strand | Q9XSM3 |
| E | Calmodulin-1 | protein | 113 | 64% helix, 0% strand | P0DP29 |
| B | Transient receptor potential cation channel subfamily V member 5 | protein | 605 | 59% helix, 5% strand | Q9XSM3 |
| C | Transient receptor potential cation channel subfamily V member 5 | protein | 606 | 61% helix, 5% strand | Q9XSM3 |
| D | Transient receptor potential cation channel subfamily V member 5 | protein | 607 | 61% helix, 5% strand | Q9XSM3 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains E
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 | 918 | 0.86 | 0.88 | 85 | empty |
| 2 | 310 | 0.85 | 0.96 | 27 | empty |
| 3 | 746 | 0.84 | 0.87 | 43 | empty |
| 4 | 550 | 0.84 | 0.89 | 56 | empty |
| 5 | 507 | 0.83 | 0.89 | 55 | empty |
Interfaces
10 interfaces between chains.
- C–D · 2984 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 2979 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 2969 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 2914 Ų buried · 24 hydrogen bonds · protein-protein
- A–E · 1933 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6DMW · Calmodulin-bound full-length RBTRPV5 · the same entry in another collection · chain E against E, TM-score 1.00
- Q9XSM3 · AlphaFold monomer V2.0 prediction for transient receptor potential cation channel… · a predicted model of the same protein · chain D against A, TM-score 0.95
- P0DP29 · AlphaFold monomer V2.0 prediction for calmodulin-1 (P0DP29) · a predicted model of the same protein · chain E against A, TM-score 0.55
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 P0DP29
- Elsewhere: RCSB PDB 6DMW · PDBe 6DMW · UniProt Q9XSM3 · UniProt P0DP29
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