Research workbench
Cycles of destabilization and repair underlie the evolution of new enzyme function
Analyse Cycles of destabilization and repair underlie the evolution of new enzyme… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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