MolNFT v1 · #124001 · protein
Pyocyanin demethylase
5K21: “Pyocyanin demethylase”. X-ray diffraction, 2 ligands (6QF, CA), 4 pockets (best druggability 0.64). MolNFT v1 #124001 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5K21
- Type
- protein
- Length
- 366 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyocyanin demethylase
- UniProt
- K0V2D8
- Ligands
- 6QF, CA
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 2% helix, 66% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyocyanin demethylase | protein | 121 | 2% helix, 68% strand | K0V2D8 |
| B | Pyocyanin demethylase | protein | 123 | 2% helix, 66% strand | K0V2D8 |
| C | Pyocyanin demethylase | protein | 122 | 2% helix, 66% strand | K0V2D8 |
Ligands and binding sites
- 6QF · phenazin-1-ol · ligand · 3 copies · chains A, B, C
- CA · Calcium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.64 | 0.91 | 23 | 6QF |
| 2 | 155 | 0.62 | 0.85 | 43 | empty |
| 3 | 136 | 0.61 | 0.85 | 28 | 6QF |
| 4 | 137 | 0.61 | 0.84 | 20 | 6QF |
Interfaces
3 interfaces between chains.
- B–C · 803 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 787 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 784 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5K21 · Pyocyanin demethylase · 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 K0V2D8
- Elsewhere: RCSB PDB 5K21 · PDBe 5K21 · UniProt K0V2D8
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