MolNFT v1 · #109792 · protein
Phosphotriesterase variant E2A
4XD6 · Phosphotriesterase variant pte-E2: “Phosphotriesterase variant E2A”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.65). MolNFT v1 #109792 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4XD6
- Type
- protein
- Length
- 659 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphotriesterase variant pte-E2
- UniProt
- A0A060GZX7
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphotriesterase variant pte-E2 | protein | 330 | 49% helix, 14% strand | A0A060GZX7 |
| G | Phosphotriesterase variant pte-E2 | protein | 329 | 49% helix, 16% strand | A0A060GZX7 |
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 · 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 | 181 | 0.65 | 0.86 | 32 | empty |
| 2 | 248 | 0.63 | 0.81 | 34 | CAC |
| 3 | 231 | 0.59 | 0.80 | 37 | CAC |
| 4 | 58 | 0.35 | 0.78 | 14 | empty |
| 5 | 62 | 0.31 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–G · 1455 Ų buried · 39 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
- 4XD6 · Phosphotriesterase Variant E2a · 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 A0A060GZX7
- Elsewhere: RCSB PDB 4XD6 · PDBe 4XD6 · UniProt A0A060GZX7
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