MolNFT v2 · #129958 · protein
Native YndL
5ONK: “Native YndL”. X-ray diffraction at 1.03, 2 ligands (ZN, SO4), 1 pocket (best druggability 0.38). MolNFT v2 #129958 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5ONK
- Type
- protein
- Length
- 202 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.03
- Source
- Bacillus subtilis
- Molecule
- YndL
- UniProt
- A0A164XNU3
- Ligands
- ZN, SO4
- Pockets
- 1 · best druggability 0.38
Structure
x-ray diffraction · resolution 1.03 · 1 distinct chain · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | YndL | protein | 202 | 37% helix, 23% strand | A0A164XNU3 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- FLC · Citrate anion · additive · chains A
- IMD · Imidazole · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 98 | 0.38 | 0.76 | 21 | SO4, FLC |
Compared structures
- 5ONK · NATIVE YNDL · 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 A0A164XNU3
- Elsewhere: RCSB PDB 5ONK · PDBe 5ONK · UniProt A0A164XNU3
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