Research workbench
Structure of human HCN4 hyperpolarization-activated cyclic nucleotide-gated ion channel in complex with cAMP
Analyse Structure of human HCN4 hyperpolarization-activated cyclic nucleotide-gated ion… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GYO
- Type
- protein
- Length
- 2,004 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.4
- Source
- Homo sapiens
- Molecule
- Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4
- UniProt
- Q9Y3Q4
- Ligands
- PC1, 3PE, CMP, PIE, UNX
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · resolution 3.4 · 1 distinct chain · 61% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4 | protein | 501 | 61% helix, 8% strand | Q9Y3Q4 |
Ligands and binding sites
- PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · 28 copies · chains A, B, D, C
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 8 copies · chains A, B, C, D
- CMP · Adenosine-3',5'-cyclic-monophosphate · ligand · 4 copies · chains A, B, C, D
- PIE · 1,2-diacyl-sn-glycero-3-phosphoinositol · ligand · 4 copies · chains A, B, C, D
- UNX · Unknown atom or ion · ion · 4 copies · chains A, D, 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1056 | 0.81 | 0.82 | 93 | empty |
| 2 | 1038 | 0.80 | 0.82 | 79 | empty |
| 3 | 928 | 0.80 | 0.82 | 72 | empty |
| 4 | 954 | 0.80 | 0.82 | 70 | empty |
| 5 | 953 | 0.79 | 0.81 | 99 | empty |
Interfaces
6 interfaces between chains.
- A–D · 3031 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 3021 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 3019 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 3015 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 352 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6GYO · Structure of human HCN4 hyperpolarization-activated cyclic nucleotide- gated ion channel… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9Y3Q4 · AlphaFold monomer V2.0 prediction for POTASSIUM/SODIUM hyperpolarization-activated cyclic… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9Y3Q4
- Elsewhere: RCSB PDB 6GYO · PDBe 6GYO · UniProt Q9Y3Q4
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