Research workbench
Opda from agrobacterium radiobacter with bound product diethyl thiophosphate from co-crystallisation with tetraethyl dithiopyrophosphate- 1.8 a
Analyse Opda from agrobacterium radiobacter with bound product diethyl thiophosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2R1P
- Type
- protein
- Length
- 328 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphotriesterase
- EC
- 3.1.8.1
- UniProt
- Q93LD7
- Ligands
- DPJ, FE2, CO
- Pockets
- 3 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphotriesterase (EC 3.1.8.1) | protein | 328 | 51% helix, 15% strand | Q93LD7 |
Ligands and binding sites
- DPJ · O,O-diethyl hydrogen thiophosphate · ligand · chains A
- FE2 · Fe (II) ion · metal · chains A
- CO · Cobalt (II) ion · metal · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 165 | 0.53 | 0.80 | 31 | DPJ, EDO |
| 2 | 70 | 0.34 | 0.76 | 16 | empty |
| 3 | 61 | 0.34 | 0.77 | 14 | empty |
Modifications
Observed in the structure: 1 modified (carboxylation).
Compared structures
- 2R1P · OpdA from Agrobacterium radiobacter with bound product diethyl thiophosphate from… · 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 Q93LD7
- Elsewhere: RCSB PDB 2R1P · PDBe 2R1P · UniProt Q93LD7
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