Research workbench
Closed-state cryo-EM structure of full-length human TRPV4 in the presence of 4a-PDD
Analyse Closed-state cryo-EM structure of full-length human TRPV4 in the presence of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8T1E
- Type
- protein
- Length
- 2,516 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.77
- 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 0.82
Structure
electron microscopy · resolution 2.77 · 1 distinct chain · 56% helix, 4% 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 | protein | 629 | 56% helix, 4% 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 · 32 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 · 3 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 | 163 | 0.82 | 0.97 | 24 | NA |
| 2 | 576 | 0.73 | 0.80 | 54 | empty |
| 3 | 594 | 0.72 | 0.80 | 52 | empty |
| 4 | 562 | 0.71 | 0.80 | 57 | 9ZR |
| 5 | 584 | 0.71 | 0.79 | 53 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2662 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 2661 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 2661 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 2651 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 18 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- Q9HBA0 · AlphaFold monomer V2.0 prediction for transient receptor potential cation channel… · a predicted model of the same protein · chain A against A, TM-score 0.94
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 8T1E · PDBe 8T1E · UniProt Q9HBA0 · UniProt C5MKY7
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