MolNFT v1 · #168379 · protein
Structure of cgmp-bound wt tax-4 reconstituted in lipid nanodiscs
6WEK · Cyclic nucleotide-gated cation channel: “Structure of cgmp-bound wt tax-4 reconstituted in lipid nanodiscs”. Electron microscopy, 3 ligands (CPL, PCG, PX2), 20 pockets (best druggability 0.81). MolNFT v1 #168379 on GenesisL1: 3D…
- PDB
- 6WEK
- Type
- protein
- Length
- 2,048 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclic nucleotide-gated cation channel
- UniProt
- Q03611
- Ligands
- CPL, PCG, PX2
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 1 distinct chain · 55% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Cyclic nucleotide-gated cation channel | protein | 512 | 55% helix, 10% strand | Q03611 |
Ligands and binding sites
- CPL · 1-palmitoyl-2-linoleoyl-sn-glycero-3-phosphocholine · ligand · 24 copies · chains A, B, C, D
- PCG · Cyclic guanosine monophosphate · ligand · 4 copies · chains A, B, C, D
- PX2 · 1,2-dilauroyl-sn-glycero-3-phosphate · ligand · 4 copies · chains A, D, B, C
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 | 1094 | 0.81 | 0.82 | 114 | CPL |
| 2 | 990 | 0.80 | 0.81 | 84 | empty |
| 3 | 996 | 0.79 | 0.81 | 57 | empty |
| 4 | 1029 | 0.78 | 0.80 | 84 | CPL |
| 5 | 715 | 0.78 | 0.82 | 71 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2481 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 2463 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 2440 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 2413 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 19 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 4 disulfide (covalent ligand, disulfide).
Compared structures
- 6WEK · Structure of cGMP-bound WT 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 B against A, TM-score 0.93
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 6WEK · PDBe 6WEK · UniProt Q03611
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