MolNFT v1 · #98601 · protein
Crystal structure of the phosphotriesterase OPHC2 from pseudomonas pseudoalcaligenes
4LE6 · Organophosphorus hydrolase: “Crystal structure of the phosphotriesterase OPHC2 from pseudomonas pseudoalcaligenes”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.85). MolNFT v1 #98601 on GenesisL1: 3D structure…
- PDB
- 4LE6
- Type
- protein
- Length
- 1,268 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Organophosphorus hydrolase
- EC
- 3.1.8.1
- UniProt
- Q5W503
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 20% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Organophosphorus hydrolase (EC 3.1.8.1) | protein | 257 | 20% helix, 32% strand | Q5W503 |
| B | Organophosphorus hydrolase (EC 3.1.8.1) | protein | 255 | 20% helix, 32% strand | Q5W503 |
| C | Organophosphorus hydrolase (EC 3.1.8.1) | protein | 254 | 19% helix, 32% strand | Q5W503 |
| D, E | Organophosphorus hydrolase (EC 3.1.8.1) | protein | 251 | 20% helix, 32% strand | Q5W503 |
Ligands and binding sites
- ZN · Zinc ion · metal · 10 copies · chains A, B, C, D, E
- GOL · Glycerol · additive · 8 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C
- PGE · Triethylene glycol · additive · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 478 | 0.85 | 0.91 | 55 | empty |
| 2 | 517 | 0.83 | 0.89 | 56 | EDO |
| 3 | 592 | 0.77 | 0.83 | 66 | GOL, PGE, EDO |
| 4 | 468 | 0.73 | 0.82 | 54 | GOL |
| 5 | 439 | 0.70 | 0.81 | 44 | empty |
Interfaces
4 interfaces between chains.
- B–C · 2557 Ų buried · 43 hydrogen bonds · protein-protein
- D–E · 2391 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 674 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 76 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 4LE6 · Crystal structure of the phosphotriesterase OPHC2 from Pseudomonas pseudoalcaligenes · 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 Q5W503
- Elsewhere: RCSB PDB 4LE6 · PDBe 4LE6 · UniProt Q5W503
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