MolNFT v1 · #168380 · protein
Structure of cgmp-unbound F403V/V407A mutant tax-4 reconstituted in lipid nanodiscs
6WEL · Cyclic nucleotide-gated cation channel: “Structure of cgmp-unbound F403V/V407A mutant tax-4 reconstituted in lipid nanodiscs”. Electron microscopy, 3 ligands (CPL, PX2, NA), 20 pockets (best druggability 0.84). MolNFT v1 #168380 on…
- PDB
- 6WEL
- Type
- protein
- Length
- 2,052 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclic nucleotide-gated cation channel
- UniProt
- Q03611
- Ligands
- CPL, PX2, NA
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 54% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Cyclic nucleotide-gated cation channel | protein | 513 | 54% helix, 11% strand | Q03611 |
Ligands and binding sites
- CPL · 1-palmitoyl-2-linoleoyl-sn-glycero-3-phosphocholine · ligand · 28 copies · chains A, B, C, D
- PX2 · 1,2-dilauroyl-sn-glycero-3-phosphate · ligand · 8 copies · chains A, D, B, C
- NA · Sodium ion · metal · 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 889 | 0.84 | 0.86 | 71 | empty |
| 2 | 1134 | 0.72 | 0.76 | 99 | empty |
| 3 | 861 | 0.68 | 0.74 | 81 | PX2 |
| 4 | 622 | 0.68 | 0.77 | 64 | empty |
| 5 | 777 | 0.67 | 0.75 | 74 | PX2 |
Interfaces
6 interfaces between chains.
- A–D · 2540 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 2536 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 2520 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 2487 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 21 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6WEL · Structure of cGMP-unbound F403V/V407A mutant TAX-4 reconstituted in lipid nanodiscs · the same entry in another collection · chain D against D, TM-score 1.00
- Q03611 · AlphaFold monomer V2.0 prediction for cyclic nucleotide-gated cation channel (Q03611) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q03611
- Elsewhere: RCSB PDB 6WEL · PDBe 6WEL · UniProt Q03611
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