MolNFT v1 · #18542 · protein

Phosphotriesterase from pseudomonas diminuta

1PSC: “Phosphotriesterase from pseudomonas diminuta”. X-ray diffraction, 2 ligands (EBP, CD), 7 pockets (best druggability 0.72). MolNFT v1 #18542 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1PSC
Type: protein
Length: 659 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phosphotriesterase
UniProt: P0A434
Ligands: EBP, CD
Pockets: 7 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 52% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phosphotriesterase	protein	329	52% helix, 15% strand	P0A434
B	Phosphotriesterase	protein	330	52% helix, 15% strand	P0A434

Ligands and binding sites

EBP · Diethyl 4-methylbenzylphosphonate · ligand · 2 copies · chains A, B
CD · Cadmium ion · metal · 4 copies · chains A, B
FMT · Formic acid · additive · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	160	0.72	0.91	28	empty
2	262	0.63	0.81	31	CD, FMT
3	245	0.63	0.81	30	CD, FMT
4	85	0.40	0.78	17	empty
5	77	0.37	0.77	16	empty

Interfaces

1 interface between chains.

A–B · 1392 Å² buried · 33 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (additive adduct).

Compared structures

1PSC · Phosphotriesterase from pseudomonas diminuta · the same entry in another collection · chain A against A, TM-score 1.00
P0A434 · AlphaFold monomer V2.0 prediction for parathion hydrolase (P0A434) · a predicted model of the same protein · 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 P0A434
Elsewhere: RCSB PDB 1PSC · PDBe 1PSC · UniProt P0A434

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