MolNFT v1 · #180538 · protein
Cryo-EM structure of rtx-bound minimal TRPV1 with nmdg at state B
7L2V · Transient receptor potential cation channel subfamily V…: “Cryo-EM structure of rtx-bound minimal TRPV1 with nmdg at state B”. Electron microscopy, 3 ligands (6EU, XPS, NA), 20 pockets (best druggability 0.83). MolNFT v1 #180538 on…
- PDB
- 7L2V
- Type
- protein
- Length
- 2,144 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, XPS, NA
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 1 distinct chain · 57% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, B, C | Transient receptor potential cation channel subfamily V member 1 | protein | 536 | 57% helix, 4% strand | O35433 |
Ligands and binding sites
- 6EU · resiniferatoxin · ligand · 4 copies · chains A, D, C, B
- XPS · 6-deoxy-6-(methylamino)-D-galactitol · ligand · chains D, B, C
- 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 | 1058 | 0.83 | 0.84 | 95 | XPS, NA |
| 2 | 1024 | 0.81 | 0.82 | 74 | empty |
| 3 | 996 | 0.81 | 0.82 | 72 | empty |
| 4 | 932 | 0.81 | 0.82 | 70 | empty |
| 5 | 856 | 0.79 | 0.82 | 72 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2285 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 2260 Ų buried · 12 hydrogen bonds · protein-protein
- D–C · 2230 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 2196 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7L2V · cryo-EM structure of RTX-bound minimal TRPV1 with NMDG at state b · 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 0.92
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 7L2V · PDBe 7L2V · UniProt O35433
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