MolNFT v1 · #182639 · protein
Cryo-EM structure of minimal TRPV1 with 2 bound rtx in opposite pockets
7MZE · Transient receptor potential cation channel subfamily V…: “Cryo-EM structure of minimal TRPV1 with 2 bound rtx in opposite pockets”. Electron microscopy, 3 ligands (XJ7, 6EU, NA), 20 pockets (best druggability 0.85). MolNFT v1…
- PDB
- 7MZE
- Type
- protein
- Length
- 2,147 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transient receptor potential cation channel subfamily V member 1
- UniProt
- O35433
- Ligands
- XJ7, 6EU, NA
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 3 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 | 537 | 58% helix, 4% strand | O35433 |
| D, B | Transient receptor potential cation channel subfamily V member 1 | protein | 536 | 58% helix, 4% strand | O35433 |
| C | Transient receptor potential cation channel subfamily V member 1 | protein | 538 | 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 · 2 copies · chains A, D, B, C
- 6EU · resiniferatoxin · ligand · 2 copies · chains D, C, A, B
- NA · Sodium ion · metal · chains A, D, B, C
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 | 271 | 0.85 | 0.96 | 32 | empty |
| 2 | 1044 | 0.81 | 0.82 | 83 | XJ7 |
| 3 | 1011 | 0.80 | 0.81 | 82 | XJ7 |
| 4 | 901 | 0.79 | 0.81 | 75 | empty |
| 5 | 704 | 0.76 | 0.81 | 74 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2716 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 2682 Ų buried · 9 hydrogen bonds · protein-protein
- D–C · 2647 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 2611 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 31 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7MZE · Cryo-EM structure of minimal TRPV1 with 2 bound RTX in opposite pockets · the same entry in another collection · chain A against A, TM-score 1.00
- O35433 · AlphaFold monomer V2.0 prediction for transient receptor potential cation channel… · a predicted model of the same protein · chain A 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 7MZE · PDBe 7MZE · UniProt O35433
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