MolNFT v1 · #181253 · protein
Cryo-EM structure of full-length TRPV1 at 4 degrees celsius
7LP9 · Transient receptor potential cation channel subfamily V…: “Cryo-EM structure of full-length TRPV1 at 4 degrees celsius”. Electron microscopy, 5 ligands (6OU, LBN, T7X), 20 pockets (best druggability 0.85). MolNFT v1 #181253 on…
- PDB
- 7LP9
- Type
- protein
- Length
- 2,536 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
- 6OU, LBN, T7X, YFP, NA
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 1 distinct chain · 56% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Transient receptor potential cation channel subfamily V member 1 | protein | 634 | 56% helix, 6% strand | O35433 |
Ligands and binding sites
- 6OU · [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate · ligand · 28 copies · chains A, D, B, C
- LBN · 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine · ligand · 8 copies · chains A, D, B, C
- T7X · Phosphatidylinositol · ligand · 4 copies · chains A, D, B, C
- YFP · 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 2 copies · chains A, B, C, D
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 | 282 | 0.85 | 0.95 | 32 | NA |
| 2 | 1019 | 0.80 | 0.81 | 84 | T7X, LBN |
| 3 | 1002 | 0.80 | 0.81 | 89 | T7X, LBN |
| 4 | 1049 | 0.80 | 0.81 | 83 | T7X, LBN |
| 5 | 846 | 0.79 | 0.82 | 74 | T7X, LBN |
Interfaces
6 interfaces between chains.
- A–D · 2953 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 2944 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 2935 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 2933 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 24 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7LP9 · Cryo-EM structure of full-length TRPV1 at 4 degrees Celsius · 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 0.95
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 7LP9 · PDBe 7LP9 · UniProt O35433
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