Research workbench
Cryo-EM structure of human cGMP-bound open CNGA1 channel in Na+/Ca2+
Analyse Cryo-EM structure of human cGMP-bound open CNGA1 channel in Na+/Ca2+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LFX
- Type
- protein
- Length
- 1,800 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.1
- Source
- Homo sapiens
- Molecule
- cGMP-gated cation channel alpha-1
- UniProt
- P29973
- Ligands
- PCG, CA
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · resolution 3.1 · 1 distinct chain · 59% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | cGMP-gated cation channel alpha-1 | protein | 450 | 59% helix, 10% strand | P29973 |
Ligands and binding sites
- PCG · Cyclic guanosine monophosphate · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 2 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1046 | 0.84 | 0.85 | 77 | CA |
| 2 | 886 | 0.75 | 0.79 | 78 | empty |
| 3 | 919 | 0.75 | 0.78 | 82 | empty |
| 4 | 832 | 0.74 | 0.78 | 67 | empty |
| 5 | 562 | 0.70 | 0.79 | 51 | empty |
Interfaces
6 interfaces between chains.
- A–D · 2812 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 2812 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 2806 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 2804 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 34 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7LFX · Cryo-EM structure of human cgmp-bound open CNGA1 channel in NA+/CA2+ · the same entry in another collection · chain D against D, TM-score 1.00
- P29973 · AlphaFold monomer V2.0 prediction for cgmp-gated cation channel alpha-1 (P29973) · a predicted model of the same protein · chain C 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 P29973
- Elsewhere: RCSB PDB 7LFX · PDBe 7LFX · UniProt P29973
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