MolNFT v1 · #143532 · protein
Phosphotriesterase variant S5 + ts analogue
6B2F: “Phosphotriesterase variant S5 + ts analogue”. X-ray diffraction, 2 ligands (HLN, ZN), 6 pockets (best druggability 0.65). MolNFT v1 #143532 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6B2F
- Type
- protein
- Length
- 644 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphotriesterase
- UniProt
- A0A060GYS1
- Ligands
- HLN, ZN
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphotriesterase | protein | 318 | 51% helix, 14% strand | A0A060GYS1 |
| G | Phosphotriesterase | protein | 326 | 51% helix, 14% strand | A0A060GYS1 |
Ligands and binding sites
- HLN · hexyl(naphthalen-2-yloxy)phosphinic acid · ligand · 2 copies · chains A, G
- ZN · Zinc ion · metal · 4 copies · chains A, G
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 6 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 | 171 | 0.65 | 0.86 | 36 | empty |
| 2 | 253 | 0.54 | 0.76 | 26 | ZN, HLN |
| 3 | 238 | 0.53 | 0.76 | 24 | HLN |
| 4 | 71 | 0.34 | 0.76 | 15 | empty |
| 5 | 78 | 0.33 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–G · 1356 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
- 6B2F · Phosphotriesterase variant S5 + TS analogue · 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 A0A060GYS1
- Elsewhere: RCSB PDB 6B2F · PDBe 6B2F · UniProt A0A060GYS1
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