MolNFT v1 · #109694 · protein
Cycles of destabilization and repair underlie evolutionary transitions in enzymes
4XAF · Phosphotriesterase variant pte-R1: “Cycles of destabilization and repair underlie evolutionary transitions in enzymes”. X-ray diffraction, 1 ligand (ZN), 6 pockets (best druggability 0.65). MolNFT v1 #109694 on GenesisL1: 3D…
- PDB
- 4XAF
- Type
- protein
- Length
- 660 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphotriesterase variant pte-R1
- UniProt
- A0A060GZX0
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphotriesterase variant pte-R1 | protein | 331 | 49% helix, 15% strand | A0A060GZX0 |
| G | Phosphotriesterase variant pte-R1 | protein | 329 | 51% helix, 15% strand | A0A060GZX0 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, G
- CAC · Cacodylate ion · additive · 2 copies · chains A, G
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 189 | 0.65 | 0.85 | 37 | empty |
| 2 | 204 | 0.59 | 0.80 | 31 | CAC, ZN |
| 3 | 210 | 0.57 | 0.79 | 30 | ZN, CAC |
| 4 | 81 | 0.37 | 0.76 | 15 | empty |
| 5 | 75 | 0.36 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–G · 1352 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
- 4XAF · 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 A0A060GZX0
- Elsewhere: RCSB PDB 4XAF · PDBe 4XAF · UniProt A0A060GZX0
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