MolNFT v1 · #121066 · protein
Bacterial sodium channel pore, 2.95 ångström resolution
5HK7 · Ion transport protein: “Bacterial sodium channel pore, 2.95 ångström resolution”. X-ray diffraction, 3 ligands (VVA, NA, CL), 3 pockets (best druggability 0.82). MolNFT v1 #121066 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5HK7
- Type
- protein
- Length
- 553 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ion transport protein
- UniProt
- Q0ABW0
- Ligands
- VVA, NA, CL
- Pockets
- 3 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 86% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ion transport protein | protein | 139 | 87% helix, 0% strand | Q0ABW0 |
| B, C, D | Ion transport protein | protein | 138 | 86% helix, 0% strand | Q0ABW0 |
Ligands and binding sites
- VVA · 2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}ethyl heptadecanoate · ligand · 10 copies · chains A, D, B, C
- NA · Sodium ion · metal · 2 copies · chains B, C
- CL · Chloride ion · ion · 2 copies · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 324 | 0.82 | 0.93 | 36 | CL |
| 2 | 1195 | 0.79 | 0.80 | 82 | VVA, NA |
| 3 | 69 | 0.34 | 0.76 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1726 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 1723 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1716 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1712 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 116 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5HK7 · Bacterial sodium channel pore, 2.95 Angstrom resolution · 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 5HK7 · PDBe 5HK7 · UniProt Q0ABW0
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