MolNFT v1 · #122530 · protein
Structure of TRPV1 determined in lipid nanodisc
5IRZ · Transient receptor potential cation channel subfamily V…: “Structure of TRPV1 determined in lipid nanodisc”. Electron microscopy, 3 ligands (6OE, 6O8, 6ES), 20 pockets (best druggability 0.82). MolNFT v1 #122530 on GenesisL1: 3D…
- PDB
- 5IRZ
- Type
- protein
- Length
- 1,576 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
- 6OE, 6O8, 6ES
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 1 distinct chain · 59% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, E, B, C | Transient receptor potential cation channel subfamily V member 1 | protein | 394 | 59% helix, 3% strand | O35433 |
Ligands and binding sites
- 6OE · (2S)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(hexanoyloxy)propyl hexanoate · ligand · 16 copies · chains D, E, B, C
- 6O8 · (4R,7S)-4-hydroxy-N,N,N-trimethyl-4,9-dioxo-7-[(pentanoyloxy)methyl]-3,5,8-trioxa-4lambda~5~-phosphatetradecan-1-aminium · ligand · 4 copies · chains D, E, B, C
- 6ES · (2S)-1-{[(R)-hydroxy{[(1R,2R,3S,4S,5S,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}-3-(pentanoyloxy)propan-2-yl decanoate · ligand · 4 copies · chains D, E, 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 183 | 0.82 | 0.97 | 31 | empty |
| 2 | 950 | 0.80 | 0.82 | 80 | 6O8, 6ES |
| 3 | 962 | 0.80 | 0.82 | 81 | 6O8, 6ES |
| 4 | 871 | 0.80 | 0.82 | 77 | 6ES |
| 5 | 882 | 0.79 | 0.82 | 79 | 6ES |
Interfaces
6 interfaces between chains.
- D–E · 2060 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 2060 Ų buried · 4 hydrogen bonds · protein-protein
- E–C · 2053 Ų buried · 4 hydrogen bonds · protein-protein
- D–B · 2051 Ų buried · 4 hydrogen bonds · protein-protein
- E–B · 46 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 covalent (covalent ligand).
Compared structures
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 5IRZ · PDBe 5IRZ · UniProt O35433
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