MolNFT v1 · #11233 · protein
High resolution structure of the cadmium-containing phosphotriesterase from pseudomonas diminuta
1JGM: “High resolution structure of the cadmium-containing phosphotriesterase from pseudomonas diminuta”. X-ray diffraction, 3 ligands (PEL, CD, NA), 5 pockets (best druggability 0.70). MolNFT v1 #11233 on GenesisL1: 3D structure, binding…
- PDB
- 1JGM
- Type
- protein
- Length
- 665 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphotriesterase
- EC
- 3.1.8.1
- UniProt
- P0A434
- Ligands
- PEL, CD, NA
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphotriesterase (EC 3.1.8.1) | protein | 333 | 50% helix, 14% strand | P0A434 |
| B | Phosphotriesterase (EC 3.1.8.1) | protein | 332 | 51% helix, 14% strand | P0A434 |
Ligands and binding sites
- PEL · 2-phenyl-ethanol · ligand · 3 copies · chains A, B
- CD · Cadmium ion · metal · 4 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 27 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 170 | 0.70 | 0.89 | 31 | empty |
| 2 | 225 | 0.63 | 0.82 | 29 | CD, EDO |
| 3 | 230 | 0.61 | 0.81 | 32 | CD, EDO |
| 4 | 67 | 0.37 | 0.78 | 14 | EDO |
| 5 | 76 | 0.35 | 0.76 | 16 | EDO |
Interfaces
1 interface between chains.
- A–B · 1334 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
- 1JGM · High Resolution Structure of the Cadmium-containing Phosphotriesterase from Pseudomonas… · 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 B 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 1JGM · PDBe 1JGM · UniProt P0A434
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