MolNFT v1 · #105733 · protein
Crystal structure of vmolac bound to 3-oxo-C10 ahl
4RDY · Parathion hydrolase: “Crystal structure of vmolac bound to 3-oxo-C10 ahl”. X-ray diffraction, 3 ligands (3M5, CO, SO4), 8 pockets (best druggability 0.85). MolNFT v1 #105733 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4RDY
- Type
- protein
- Length
- 627 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Parathion hydrolase
- UniProt
- F0QXN6
- Ligands
- 3M5, CO, SO4
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Parathion hydrolase | protein | 313 | 50% helix, 13% strand | F0QXN6 |
| B | Parathion hydrolase | protein | 314 | 49% helix, 13% strand | F0QXN6 |
Ligands and binding sites
- 3M5 · 3-oxo-N-[(3S)-2-oxotetrahydrofuran-3-yl]decanamide · ligand · 2 copies · chains A, B
- CO · Cobalt (II) ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 13 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 470 | 0.85 | 0.91 | 37 | GOL |
| 2 | 153 | 0.61 | 0.84 | 29 | 3M5 |
| 3 | 162 | 0.60 | 0.83 | 28 | 3M5 |
| 4 | 141 | 0.48 | 0.78 | 24 | GOL |
| 5 | 159 | 0.48 | 0.77 | 28 | GOL, SO4 |
Interfaces
1 interface between chains.
- A–B · 1760 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
- 4RDY · Crystal structure of VmoLac bound to 3-oxo-C10 AHL · the same entry in another collection · chain B against B, 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 F0QXN6
- Elsewhere: RCSB PDB 4RDY · PDBe 4RDY · UniProt F0QXN6
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