Research workbench
Cryo-EM structure of human rod CNGA1/B1 channel in L-cis-Diltiazem-blocked open state
Analyse Cryo-EM structure of human rod CNGA1/B1 channel in L-cis-Diltiazem-blocked open… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RHJ
- Type
- protein
- Length
- 1,783 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.88
- Source
- Homo sapiens
- Molecule
- cGMP-gated cation channel alpha-1; Cyclic nucleotide-gated cation channel beta-1
- UniProt
- P29973, Q14028
- Ligands
- PCG, 5H0
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · resolution 2.88 · 2 distinct chains · 59% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | cGMP-gated cation channel alpha-1 | protein | 450 | 60% helix, 11% strand | P29973 |
| B | Cyclic nucleotide-gated cation channel beta-1 | protein | 433 | 59% helix, 12% strand | Q14028 |
Ligands and binding sites
- PCG · Cyclic guanosine monophosphate · ligand · 4 copies · chains A, B, C, D
- 5H0 · (2R,3R)-5-[2-(dimethylamino)ethyl]-2-(4-methoxyphenyl)-4-oxo-2,3,4,5-tetrahydro-1,5-benzothiazepin-3-yl acetate · ligand · 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 | 554 | 0.82 | 0.88 | 58 | 5H0 |
| 2 | 701 | 0.78 | 0.82 | 84 | empty |
| 3 | 616 | 0.76 | 0.82 | 74 | empty |
| 4 | 573 | 0.75 | 0.82 | 67 | empty |
| 5 | 368 | 0.70 | 0.82 | 46 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2848 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 2784 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 2746 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 2724 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 29 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7RHJ · Cryo-EM structure of human rod CNGA1/B1 channel in L-cis-diltiazem- blocked open state · 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 A against A, TM-score 0.94
- Q14028 · AlphaFold monomer V2.0 prediction for cyclic nucleotide-gated cation channel beta-1… · a predicted model of the same protein · chain B against A, TM-score 0.91
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
- Every structure of UniProt Q14028
- Elsewhere: RCSB PDB 7RHJ · PDBe 7RHJ · UniProt P29973 · UniProt Q14028
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