Research workbench
Phosphotriesterase variant R18DELTAL7
Analyse Phosphotriesterase variant R18DELTAL7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BHK
- Type
- protein
- Length
- 1,273 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphotriesterase
- UniProt
- A0A060GYS7
- Ligands
- ZN
- Pockets
- 12 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphotriesterase | protein | 318 | 50% helix, 16% strand | A0A060GYS7 |
| G | Phosphotriesterase | protein | 316 | 52% helix, 15% strand | A0A060GYS7 |
| B | Phosphotriesterase | protein | 320 | 50% helix, 16% strand | A0A060GYS7 |
| E | Phosphotriesterase | protein | 319 | 51% helix, 15% strand | A0A060GYS7 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, G, B, E
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 14 copies · chains A, G, E, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 314 | 0.67 | 0.82 | 31 | MPD |
| 2 | 399 | 0.65 | 0.79 | 58 | empty |
| 3 | 134 | 0.65 | 0.88 | 32 | empty |
| 4 | 256 | 0.60 | 0.79 | 29 | MPD |
| 5 | 240 | 0.58 | 0.79 | 29 | MPD |
Interfaces
3 interfaces between chains.
- A–G · 1481 Ų buried · 38 hydrogen bonds · protein-protein
- B–E · 1440 Ų buried · 37 hydrogen bonds · protein-protein
- G–E · 364 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 6BHK · Phosphotriesterase variant R18deltaL7 · 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 6BHK · PDBe 6BHK · UniProt A0A060GYS7
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