Research workbench
Cryo-EM structure of minimal TRPV1 with 3 bound rtx and 1 perturbed pi
Analyse Cryo-EM structure of minimal TRPV1 with 3 bound rtx and 1 perturbed pi in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MZB
- Type
- protein
- Length
- 2,145 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
- 6EU, XJ7, NA
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 2 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, C | Transient receptor potential cation channel subfamily V member 1 | protein | 536 | 59% helix, 4% strand | O35433 |
Ligands and binding sites
- 6EU · resiniferatoxin · ligand · 3 copies · chains D, C, A, B
- 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 · chains A, D
- 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 265 | 0.85 | 0.96 | 29 | empty |
| 2 | 1140 | 0.81 | 0.82 | 88 | XJ7 |
| 3 | 757 | 0.80 | 0.83 | 65 | empty |
| 4 | 731 | 0.77 | 0.82 | 87 | empty |
| 5 | 805 | 0.76 | 0.80 | 73 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2699 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 2695 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 2672 Ų buried · 9 hydrogen bonds · protein-protein
- D–C · 2663 Ų buried · 7 hydrogen bonds · protein-protein
- D–B · 23 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7MZB · Cryo-EM structure of minimal TRPV1 with 3 bound RTX and 1 perturbed PI · 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 7MZB · PDBe 7MZB · UniProt O35433
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.