MolNFT v1 · #120547 · protein
Structure of a eukaryotic cyclic nucleotide-gated channel
5H3O · Cyclic nucleotide-gated cation channel: “Structure of a eukaryotic cyclic nucleotide-gated channel”. Electron microscopy, 2 ligands (PCG, NA), 20 pockets (best druggability 0.81). MolNFT v1 #120547 on GenesisL1: 3D structure…
- PDB
- 5H3O
- Type
- protein
- Length
- 2,040 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclic nucleotide-gated cation channel
- UniProt
- Q03611
- Ligands
- PCG, NA
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 1 distinct chain · 54% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Cyclic nucleotide-gated cation channel | protein | 510 | 54% helix, 10% strand | Q03611 |
Ligands and binding sites
- PCG · Cyclic guanosine monophosphate · ligand · 4 copies · chains A, B, C, D
- 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 | 936 | 0.81 | 0.83 | 56 | NA |
| 2 | 662 | 0.74 | 0.80 | 64 | empty |
| 3 | 639 | 0.73 | 0.80 | 65 | empty |
| 4 | 622 | 0.73 | 0.80 | 66 | empty |
| 5 | 617 | 0.72 | 0.80 | 62 | empty |
Interfaces
6 interfaces between chains.
- A–D · 2723 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 2723 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 2720 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 2718 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 23 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5H3O · Structure of a eukaryotic cyclic nucleotide-gated channel · 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 C against A, TM-score 0.92
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 5H3O · PDBe 5H3O · UniProt Q03611
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