Research workbench
Cryo-EM structure of cGMP bound human CNGA3/CNGB3 channel in GDN, transition state 1
Analyse Cryo-EM structure of cGMP bound human CNGA3/CNGB3 channel in GDN, transition… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8EU3
- Type
- protein
- Length
- 1,770 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.62
- Source
- Homo sapiens
- Molecule
- Cyclic nucleotide-gated cation channel alpha-3; Cyclic nucleotide-gated cation channel…
- UniProt
- Q16281, Q9NQW8
- Ligands
- PCG, NAG
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · resolution 3.62 · 4 distinct chains · 60% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclic nucleotide-gated cation channel alpha-3 | protein | 444 | 60% helix, 7% strand | Q16281 |
| B | Cyclic nucleotide-gated cation channel alpha-3 | protein | 443 | 60% helix, 8% strand | Q16281 |
| C | Cyclic nucleotide-gated cation channel alpha-3 | protein | 445 | 59% helix, 8% strand | Q16281 |
| D | Cyclic nucleotide-gated cation channel beta-3 | protein | 438 | 62% helix, 9% strand | Q9NQW8 |
Ligands and binding sites
- PCG · Cyclic guanosine monophosphate · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, 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 | 1025 | 0.79 | 0.81 | 107 | empty |
| 2 | 188 | 0.79 | 0.93 | 34 | empty |
| 3 | 124 | 0.77 | 0.95 | 24 | empty |
| 4 | 571 | 0.75 | 0.82 | 58 | empty |
| 5 | 528 | 0.75 | 0.83 | 63 | empty |
Interfaces
5 interfaces between chains.
- B–C · 2806 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 2744 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 2738 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 2713 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 40 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 glycan (N-glycosylation).
Compared structures
- Q16281 · AlphaFold monomer V2.0 prediction for cyclic nucleotide-gated cation channel alpha-3… · a predicted model of the same protein · chain B against A, TM-score 0.96
- Q9NQW8 · AlphaFold monomer V2.0 prediction for cyclic nucleotide-gated cation channel beta-3… · a predicted model of the same protein · chain D 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 Q16281
- Every structure of UniProt Q9NQW8
- Elsewhere: RCSB PDB 8EU3 · PDBe 8EU3 · UniProt Q16281 · UniProt Q9NQW8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.