Research workbench
Crystal structure of the unliganded form of HCN2 cnbd
Analyse Crystal structure of the unliganded form of HCN2 cnbd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JON
- Type
- protein
- Length
- 1,015 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltose-binding periplasmic PROTEIN,POTASSIUM/SODIUM hyperpolarization-activated cyclic…
- UniProt
- P0AEY0, O88703
- Ligands
- GLC, NO3
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Maltose-binding periplasmic PROTEIN,POTASSIUM/SODIUM hyperpolarization-activated cyclic nucleotide-gated channel 2 | protein | 509 | 44% helix, 22% strand | P0AEY0, O88703 |
| B | Maltose-binding periplasmic PROTEIN,POTASSIUM/SODIUM hyperpolarization-activated cyclic nucleotide-gated channel 2 | protein | 506 | 44% helix, 23% strand | P0AEY0, O88703 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B
- NO3 · Nitrate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1113 | 0.76 | 0.78 | 84 | empty |
| 2 | 269 | 0.73 | 0.87 | 31 | GLC |
| 3 | 275 | 0.71 | 0.85 | 31 | GLC |
| 4 | 480 | 0.63 | 0.76 | 39 | empty |
| 5 | 551 | 0.63 | 0.75 | 38 | empty |
Interfaces
1 interface between chains.
- A–B · 635 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5JON · Crystal structure of the unliganded form of HCN2 CNBD · 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 0.32
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 P0AEY0
- Every structure of UniProt O88703
- Elsewhere: RCSB PDB 5JON · PDBe 5JON · UniProt P0AEY0 · UniProt O88703
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