MolNFT v1 · #124517 · protein
HCN2 cnbd in complex with uridine-3', 5'-cyclic monophosphate (cump)
5KHJ · POTASSIUM/SODIUM hyperpolarization-activated cyclic…: “HCN2 cnbd in complex with uridine-3', 5'-cyclic monophosphate (cump)”. X-ray diffraction, 1 ligand (6SY), 5 pockets (best druggability 0.74). MolNFT v1 #124517 on GenesisL1: 3D…
- PDB
- 5KHJ
- Type
- protein
- Length
- 400 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- POTASSIUM/SODIUM hyperpolarization-activated cyclic nucleotide-gated channel 2
- UniProt
- O88703
- Ligands
- 6SY
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | POTASSIUM/SODIUM hyperpolarization-activated cyclic nucleotide-gated channel 2 | protein | 199 | 51% helix, 19% strand | O88703 |
| B | POTASSIUM/SODIUM hyperpolarization-activated cyclic nucleotide-gated channel 2 | protein | 201 | 51% helix, 18% strand | O88703 |
Ligands and binding sites
- 6SY · Uridine-3',5'-cyclic monophosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 88 | 0.74 | 0.96 | 21 | 6SY |
| 2 | 95 | 0.72 | 0.94 | 18 | 6SY |
| 3 | 375 | 0.65 | 0.79 | 29 | empty |
| 4 | 312 | 0.64 | 0.80 | 27 | empty |
| 5 | 333 | 0.53 | 0.74 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 1165 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5KHJ · HCN2 CNBD in complex with uridine-3', 5'-cyclic monophosphate (cUMP) · the same entry in another collection · chain A against A, TM-score 1.00
- O88703 · AlphaFold monomer V2.0 prediction for POTASSIUM/SODIUM hyperpolarization-activated cyclic… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 O88703
- Elsewhere: RCSB PDB 5KHJ · PDBe 5KHJ · UniProt O88703
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