Research workbench
Structural basis for natural lactonase and promiscuous phosphotriesterase activities
Analyse Structural basis for natural lactonase and promiscuous phosphotriesterase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VC7
- Type
- protein
- Length
- 1,256 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aryldialkylphosphatase
- EC
- 3.1.8.1
- UniProt
- Q97VT7
- Ligands
- HT5, FE2, CO
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Aryldialkylphosphatase (EC 3.1.8.1) | protein | 314 | 46% helix, 14% strand | Q97VT7 |
Ligands and binding sites
- HT5 · (4S)-4-(decanoylamino)-5-hydroxy-3,4-dihydro-2H-thiophenium · ligand · 4 copies · chains A, B, C, D
- FE2 · Fe (II) ion · metal · 4 copies · chains A, B, C, D
- CO · Cobalt (II) ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 28 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · 25 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 804 | 0.83 | 0.85 | 85 | CO, GOL, EDO, HT5 |
| 2 | 359 | 0.82 | 0.91 | 30 | GOL, EDO |
| 3 | 402 | 0.74 | 0.84 | 60 | GOL, HT5 |
| 4 | 232 | 0.72 | 0.87 | 36 | CO, GOL, HT5 |
| 5 | 412 | 0.67 | 0.79 | 47 | EDO, HT5 |
Interfaces
3 interfaces between chains.
- C–D · 1878 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 1867 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 436 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 2VC7 · Structural basis for natural lactonase and promiscuous phosphotriesterase activities · the same entry in another collection · chain A against A, TM-score 1.00
- Q97VT7 · AlphaFold monomer V2.0 prediction for aryldialkylphosphatase (Q97VT7) · a predicted model of the same protein · 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 Q97VT7
- Elsewhere: RCSB PDB 2VC7 · PDBe 2VC7 · UniProt Q97VT7
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