MolNFT v1 · #56377 · protein
Structure of a bacterial cyclic-nucleotide regulated ion channel
2ZD9 · MLL3241 protein: “Structure of a bacterial cyclic-nucleotide regulated ion channel”. X-ray diffraction, 1 ligand (K), 13 pockets (best druggability 0.61). MolNFT v1 #56377 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2ZD9
- Type
- protein
- Length
- 913 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MLL3241 protein
- UniProt
- Q98GN8
- Ligands
- K
- Pockets
- 13 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 67% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MLL3241 protein | protein | 223 | 69% helix, 0% strand | Q98GN8 |
| B | MLL3241 protein | protein | 231 | 67% helix, 0% strand | Q98GN8 |
| C | MLL3241 protein | protein | 234 | 64% helix, 0% strand | Q98GN8 |
| D | MLL3241 protein | protein | 225 | 68% helix, 0% strand | Q98GN8 |
Ligands and binding sites
- K · Potassium ion · metal · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 386 | 0.61 | 0.76 | 44 | empty |
| 2 | 364 | 0.58 | 0.75 | 42 | empty |
| 3 | 309 | 0.57 | 0.76 | 32 | empty |
| 4 | 342 | 0.57 | 0.75 | 32 | empty |
| 5 | 136 | 0.43 | 0.75 | 14 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1899 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1894 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1803 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 1782 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 115 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2ZD9 · Structure of a Bacterial Cyclic-Nucleotide Regulated Ion Channel · the same entry in another collection · chain D against D, TM-score 1.00
- Q98GN8 · AlphaFold monomer V2.0 prediction for cyclic nucleotide-gated potassium channel MLL3241… · a predicted model of the same protein · chain A against A, TM-score 0.93
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 Q98GN8
- Elsewhere: RCSB PDB 2ZD9 · PDBe 2ZD9 · UniProt Q98GN8
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