MolNFT v1 · #121072 · protein
Bacterial sodium channel neck 7G mutant
5HKD · Ion transport protein: “Bacterial sodium channel neck 7G mutant”. X-ray diffraction, 1 ligand (CA), 3 pockets (best druggability 0.79). MolNFT v1 #121072 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5HKD
- Type
- protein
- Length
- 483 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ion transport protein
- UniProt
- Q0ABW0
- Ligands
- CA
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ion transport protein | protein | 121 | 71% helix, 0% strand | Q0ABW0 |
| B | Ion transport protein | protein | 116 | 76% helix, 0% strand | Q0ABW0 |
| C, D | Ion transport protein | protein | 123 | 72% helix, 0% strand | Q0ABW0 |
Ligands and binding sites
- CA · Calcium ion · metal · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1070 | 0.79 | 0.80 | 85 | empty |
| 2 | 125 | 0.53 | 0.81 | 20 | empty |
| 3 | 124 | 0.53 | 0.82 | 19 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1317 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1272 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1197 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 1195 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 98 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5HKD · Bacterial sodium channel neck 7G mutant · the same entry in another collection · chain A against A, TM-score 1.00
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 Q0ABW0
- Elsewhere: RCSB PDB 5HKD · PDBe 5HKD · UniProt Q0ABW0
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