MolNFT v2 · #220468 · protein
Cryo-EM structure of full-length human TRPV4 in apo state
8T1B · Transient receptor potential cation channel subfamily V…: “Cryo-EM structure of full-length human TRPV4 in apo state”. Electron microscopy at 3.0, 3 ligands (9ZR, YJ0, NA), 20 pockets (best druggability 0.79). MolNFT v2 #220468 on…
- PDB
- 8T1B
- Type
- protein
- Length
- 2,576 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.0
- Source
- Homo sapiens; Human betaherpesvirus 5
- Molecule
- Transient receptor potential cation channel subfamily V member 4/Enhanced green…
- UniProt
- Q9HBA0, C5MKY7
- Ligands
- 9ZR, YJ0, NA
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · resolution 3.0 · 1 distinct chain · 51% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Transient receptor potential cation channel subfamily V member 4/Enhanced green fluorescent protein chimera | protein | 644 | 51% helix, 5% strand | Q9HBA0, C5MKY7 |
Ligands and binding sites
- 9ZR · [(2~{R})-2-[(~{Z})-hexadec-9-enoyl]oxy-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy-propyl] (~{Z})-docos-13-enoate · ligand · 40 copies · chains A, B, D, C
- YJ0 · (2R)-2-{[(4-O-hexopyranosyl-beta-D-glucopyranosyl)oxy]methyl}-4-{[(25R)-5beta,14beta,17beta-spirostan-3beta-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside · ligand · 8 copies · chains A, D, B, C
- NA · Sodium ion · metal · 4 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 | 138 | 0.79 | 0.96 | 28 | NA |
| 2 | 476 | 0.69 | 0.79 | 43 | empty |
| 3 | 442 | 0.69 | 0.80 | 39 | empty |
| 4 | 446 | 0.68 | 0.79 | 38 | empty |
| 5 | 423 | 0.68 | 0.80 | 41 | empty |
Interfaces
6 interfaces between chains.
- A–D · 3056 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 3005 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 2996 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 2996 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 17 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
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 Q9HBA0
- Every structure of UniProt C5MKY7
- Elsewhere: RCSB PDB 8T1B · PDBe 8T1B · UniProt Q9HBA0 · UniProt C5MKY7
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