Research workbench
Crystal structure of phosphotriesterase homology protein from escherichia COLI complexed with phosphate in active site
Analyse Crystal structure of phosphotriesterase homology protein from escherichia COLI… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LEF
- Type
- protein
- Length
- 2,323 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphotriesterase homology protein
- UniProt
- P45548
- Ligands
- BGC, ZN, PO4
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D, B, E, H | Phosphotriesterase homology protein | protein | 290 | 51% helix, 16% strand | P45548 |
| A, F, G | Phosphotriesterase homology protein | protein | 291 | 50% helix, 16% strand | P45548 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · chains C, B
- ZN · Zinc ion · metal · 16 copies · chains C, D, A, B, E, F, G, H
- PO4 · Phosphate ion · ion · 31 copies · chains C, D, A, B, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1165 | 0.74 | 0.77 | 99 | empty |
| 2 | 313 | 0.64 | 0.80 | 29 | empty |
| 3 | 240 | 0.62 | 0.82 | 29 | BGC |
| 4 | 236 | 0.61 | 0.81 | 33 | ZN, PO4 |
| 5 | 251 | 0.60 | 0.80 | 34 | PO4 |
Interfaces
10 interfaces between chains.
- D–A · 456 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 376 Ų buried · 1 hydrogen bond · protein-protein
- F–G · 351 Ų buried · 2 hydrogen bonds · protein-protein
- B–F · 335 Ų buried · 4 hydrogen bonds · protein-protein
- C–B · 331 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4LEF · Crystal structure of PHOSPHOTRIESTERASE HOMOLOGY PROTEIN FROM ESCHERICHIA COLI complexed… · the same entry in another collection · chain H against H, TM-score 1.00
- P45548 · AlphaFold monomer V2.0 prediction for phosphotriesterase homology protein (P45548) · 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 P45548
- Elsewhere: RCSB PDB 4LEF · PDBe 4LEF · UniProt P45548
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