Research workbench
Cryo-EM structure of human rod CNGA1/B1 channel in L-cis-diltiazem- trapped closed state
Analyse Cryo-EM structure of human rod CNGA1/B1 channel in L-cis-diltiazem- trapped… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RHK
- Type
- protein
- Length
- 1,776 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cgmp-gated cation channel alpha-1; Cyclic nucleotide-gated cation channel beta-1
- UniProt
- P29973, Q14028
- Ligands
- PCG, 5H0
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 3 distinct chains · 60% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Cgmp-gated cation channel alpha-1 | protein | 450 | 61% helix, 9% strand | P29973 |
| B | Cyclic nucleotide-gated cation channel beta-1 | protein | 418 | 59% helix, 13% strand | Q14028 |
| A, D | Cgmp-gated cation channel alpha-1 | protein | 454 | 60% helix, 9% strand | P29973 |
Ligands and binding sites
- PCG · Cyclic guanosine monophosphate · ligand · 4 copies · chains C, B, A, 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 C, B, A, 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 215 | 0.83 | 0.95 | 30 | 5H0 |
| 2 | 620 | 0.76 | 0.82 | 82 | empty |
| 3 | 439 | 0.76 | 0.85 | 47 | empty |
| 4 | 524 | 0.74 | 0.82 | 65 | empty |
| 5 | 447 | 0.70 | 0.81 | 67 | empty |
Interfaces
6 interfaces between chains.
- A–D · 2946 Ų buried · 20 hydrogen bonds · protein-protein
- C–B · 2936 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 2896 Ų buried · 20 hydrogen bonds · protein-protein
- B–A · 2860 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 105 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7RHK · Cryo-EM structure of human rod CNGA1/B1 channel in L-cis-Diltiazem-trapped closed 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 0.91
- 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 0.90
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 7RHK · PDBe 7RHK · UniProt P29973 · UniProt Q14028
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