Research workbench

Opda from agrobacterium radiobacter with bound product dimethylthiophosphate

Analyse Opda from agrobacterium radiobacter with bound product dimethylthiophosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2D2G
Type: protein
Length: 329 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: DZZ, CO
Pockets: 3 · best druggability 0.53

Structure

x-ray diffraction · 1 distinct chain · 51% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phosphotriesterase (EC 3.1.8.1)	protein	329	51% helix, 14% strand	Q93LD7

Ligands and binding sites

DZZ · O,O-dimethyl hydrogen thiophosphate · ligand · chains A
CO · Cobalt (II) ion · metal · 2 copies · 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	168	0.53	0.79	31	DZZ
2	80	0.35	0.76	17	empty
3	51	0.34	0.79	11	empty

Modifications

Observed in the structure: 1 modified (carboxylation).

Compared structures

2D2G · OpdA from Agrobacterium radiobacter with bound product dimethylthiophosphate · 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 2D2G · PDBe 2D2G · UniProt Q93LD7

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