Research workbench
Crystal structure and computational analyses provide insights into the catalytic mechanism of 2, 4-diacetylphloroglucinol hydrolase phlg from pseudomonas fluorescens
Analyse Crystal structure and computational analyses provide insights into the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HWP
- Type
- protein
- Length
- 576 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phlg
- UniProt
- Q4K423
- Ligands
- ZN, NI, CL
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phlg | protein | 288 | 42% helix, 25% strand | Q4K423 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.81 | 0.98 | 25 | empty |
| 2 | 105 | 0.80 | 0.98 | 26 | empty |
| 3 | 155 | 0.59 | 0.83 | 36 | empty |
| 4 | 109 | 0.56 | 0.84 | 18 | empty |
| 5 | 110 | 0.51 | 0.81 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1334 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 3HWP · Crystal structure and computational analyses provide insights into the catalytic… · the same entry in another collection · chain A against A, TM-score 1.00
- Q4K423 · AlphaFold monomer V2.0 prediction for 2,4-diacetylphloroglucinol hydrolase (Q4K423) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q4K423
- Elsewhere: RCSB PDB 3HWP · PDBe 3HWP · UniProt Q4K423
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