MolNFT v1 · #109790 · protein
Phosphotriesterase variant E2B
4XD4 · Phosphotriesterase variant pte-R3: “Phosphotriesterase variant E2B”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.65). MolNFT v1 #109790 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4XD4
- Type
- protein
- Length
- 658 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphotriesterase variant pte-R3
- UniProt
- A0A060GSX0
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Phosphotriesterase variant pte-R3 | protein | 329 | 50% helix, 13% strand | A0A060GSX0 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, G
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A, G
- CAC · Cacodylate ion · additive · 2 copies · chains A, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 171 | 0.65 | 0.86 | 33 | empty |
| 2 | 221 | 0.60 | 0.81 | 35 | CAC |
| 3 | 214 | 0.59 | 0.80 | 31 | CAC, ZN |
| 4 | 84 | 0.38 | 0.77 | 16 | empty |
| 5 | 78 | 0.37 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–G · 1433 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
- 4XD4 · Phosphotriesterase variant E2b · 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 A0A060GSX0
- Elsewhere: RCSB PDB 4XD4 · PDBe 4XD4 · UniProt A0A060GSX0
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