Research workbench
Crystal structure of a lactonase mutant in complex with substrate B
Analyse Crystal structure of a lactonase mutant in complex with substrate B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IE6
- Type
- protein
- Length
- 655 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Zearalenone hydrolase
- UniProt
- Q8NKB0
- Ligands
- ZHB
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Zearalenone hydrolase | protein | 264 | 49% helix, 19% strand | Q8NKB0 |
| C | Zearalenone hydrolase | protein | 127 | 28% helix, 13% strand | Q8NKB0 |
Ligands and binding sites
- ZHB · (3S,7S,11E)-7,14,16-trihydroxy-3-methyl-3,4,5,6,7,8,9,10-octahydro-1H-2-benzoxacyclotetradecin-1-one · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 297 | 0.77 | 0.89 | 34 | ZHB |
| 2 | 312 | 0.76 | 0.87 | 36 | ZHB |
| 3 | 459 | 0.64 | 0.77 | 51 | empty |
| 4 | 174 | 0.59 | 0.81 | 17 | empty |
| 5 | 181 | 0.58 | 0.81 | 27 | empty |
Interfaces
3 interfaces between chains.
- A–B · 672 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 247 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 130 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5IE6 · Crystal structure of a lactonase mutant in complex with substrate b · 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 Q8NKB0
- Elsewhere: RCSB PDB 5IE6 · PDBe 5IE6 · UniProt Q8NKB0
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