Research workbench
Cryo-EM structure of minimal TRPV1 with 1 partially bound RTX
Analyse Cryo-EM structure of minimal TRPV1 with 1 partially bound RTX in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MZ9
- Type
- protein
- Length
- 2,278 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.18
- Source
- Rattus norvegicus
- Molecule
- Transient receptor potential cation channel subfamily V member 1
- UniProt
- O35433
- Ligands
- XJ7, 6EU, NA
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · resolution 3.18 · 4 distinct chains · 58% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transient receptor potential cation channel subfamily V member 1 | protein | 538 | 58% helix, 4% strand | O35433 |
| D | Transient receptor potential cation channel subfamily V member 1 | protein | 537 | 58% helix, 4% strand | O35433 |
| C | Transient receptor potential cation channel subfamily V member 1 | protein | 619 | 58% helix, 4% strand | O35433 |
| B | Transient receptor potential cation channel subfamily V member 1 | protein | 584 | 58% helix, 4% strand | O35433 |
Ligands and binding sites
- XJ7 · (2S)-1-(butanoyloxy)-3-{[(R)-hydroxy{[(1r,2r,3s,4s,5r, 6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propan-2-yl tridecanoate · ligand · 3 copies · chains D, C, B, A
- 6EU · resiniferatoxin · ligand · chains A, D
- NA · Sodium ion · metal · chains A, D, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 249 | 0.84 | 0.96 | 32 | empty |
| 2 | 1016 | 0.80 | 0.81 | 87 | XJ7 |
| 3 | 1059 | 0.80 | 0.81 | 79 | XJ7 |
| 4 | 1106 | 0.78 | 0.80 | 110 | XJ7 |
| 5 | 447 | 0.74 | 0.83 | 38 | empty |
Interfaces
6 interfaces between chains.
- A–D · 2708 Ų buried · 7 hydrogen bonds · protein-protein
- D–C · 2687 Ų buried · 8 hydrogen bonds · protein-protein
- C–B · 2682 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 2654 Ų buried · 5 hydrogen bonds · protein-protein
- D–B · 33 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7MZ9 · Cryo-EM structure of minimal TRPV1 with 1 partially bound rtx · the same entry in another collection · chain D against D, TM-score 1.00
- O35433 · AlphaFold monomer V2.0 prediction for transient receptor potential cation channel… · a predicted model of the same protein · chain D against A, TM-score 0.97
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 O35433
- Elsewhere: RCSB PDB 7MZ9 · PDBe 7MZ9 · UniProt O35433
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