Research workbench
Discovery and structural analysis of a phloretin hydrolase from the opportunistic pathogen mycobacterium abscessus
Analyse Discovery and structural analysis of a phloretin hydrolase from the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XEY
- Type
- protein
- Length
- 1,059 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phloretin hydrolase
- UniProt
- B1MK49
- Ligands
- 83X
- Pockets
- 19 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phloretin hydrolase | protein | 277 | 38% helix, 25% strand | B1MK49 |
| B | Phloretin hydrolase | protein | 273 | 36% helix, 26% strand | B1MK49 |
| C | Phloretin hydrolase | protein | 259 | 36% helix, 28% strand | B1MK49 |
| D | Phloretin hydrolase | protein | 250 | 37% helix, 28% strand | B1MK49 |
Ligands and binding sites
- 83X · 1-[2,4,6-tris(oxidanyl)phenyl]ethanone · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 80 | 0.77 | 0.99 | 23 | 83X |
| 2 | 80 | 0.76 | 0.98 | 18 | empty |
| 3 | 75 | 0.75 | 0.98 | 23 | empty |
| 4 | 72 | 0.75 | 0.98 | 22 | empty |
| 5 | 112 | 0.74 | 0.94 | 27 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1382 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 397 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 86 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5XEY · Discovery and structural analysis of a phloretin hydrolase from the opportunistic… · the same entry in another collection · chain D against D, TM-score 1.00
- B1MK49 · AlphaFold monomer V2.0 prediction for phloretin hydrolase (B1MK49) · a predicted model of the same protein · chain D 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 B1MK49
- Elsewhere: RCSB PDB 5XEY · PDBe 5XEY · UniProt B1MK49
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