MolNFT v1 · #109695 · protein
Cycles of destabilization and repair underlie the evolution of new enzyme function
4XAG · Phosphotriesterase variant pte-R6: “Cycles of destabilization and repair underlie the evolution of new enzyme function”. X-ray diffraction, 1 ligand (ZN), 7 pockets (best druggability 0.65). MolNFT v1 #109695 on GenesisL1: 3D…
- PDB
- 4XAG
- Type
- protein
- Length
- 658 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphotriesterase variant pte-R6
- UniProt
- A0A060GPQ0
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Phosphotriesterase variant pte-R6 | protein | 329 | 48% helix, 16% strand | A0A060GPQ0 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, G
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 copies · chains A, G
- CAC · Cacodylate ion · additive · chains G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 157 | 0.65 | 0.86 | 26 | empty |
| 2 | 214 | 0.63 | 0.83 | 25 | CAC, ZN |
| 3 | 254 | 0.60 | 0.80 | 37 | MPD |
| 4 | 67 | 0.36 | 0.77 | 14 | empty |
| 5 | 71 | 0.34 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–G · 1427 Ų buried · 39 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
- 4XAG · Cycles of destabilization and repair underlie the evolution of new enzyme function · 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 A0A060GPQ0
- Elsewhere: RCSB PDB 4XAG · PDBe 4XAG · UniProt A0A060GPQ0
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