Research workbench
Cycles of destabilization and repair underlie evolutionary transitions in enzymes
Analyse Cycles of destabilization and repair underlie evolutionary transitions in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XAZ
- Type
- protein
- Length
- 655 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphotriesterase variant pte-R18
- UniProt
- A0A060GYS7
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphotriesterase variant pte-R18 | protein | 328 | 52% helix, 15% strand | A0A060GYS7 |
| G | Phosphotriesterase variant pte-R18 | protein | 327 | 50% helix, 14% strand | A0A060GYS7 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, G
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 245 | 0.65 | 0.82 | 43 | empty |
| 2 | 219 | 0.60 | 0.81 | 29 | empty |
| 3 | 135 | 0.49 | 0.79 | 30 | empty |
| 4 | 70 | 0.34 | 0.76 | 18 | empty |
| 5 | 58 | 0.32 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–G · 1439 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
- 4XAZ · Cycles of destabilization and repair underlie evolutionary transitions in enzymes · 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 A0A060GYS7
- Elsewhere: RCSB PDB 4XAZ · PDBe 4XAZ · UniProt A0A060GYS7
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