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Crystal structure of Baeyer-Villiger monooxygenase from Parvibaculum lavamentivorans
Analyse Crystal structure of Baeyer-Villiger monooxygenase from Parvibaculum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JDK
- Type
- protein
- Length
- 1,030 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.495
- Source
- Parvibaculum lavamentivorans (strain DS-1 / DSM 13023 / NCIMB 13966)
- Molecule
- Baeyer-Villiger monooxygenase
- EC
- 1.14.13.-
- UniProt
- A7HU16
- Ligands
- FAD, MG
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · resolution 2.495 · 2 distinct chains · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Baeyer-Villiger monooxygenase (EC 1.14.13.-) | protein | 514 | 36% helix, 20% strand | A7HU16 |
| B | Baeyer-Villiger monooxygenase (EC 1.14.13.-) | protein | 516 | 35% helix, 20% strand | A7HU16 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1054 | 0.83 | 0.84 | 101 | FAD |
| 2 | 1070 | 0.82 | 0.83 | 90 | FAD |
| 3 | 363 | 0.67 | 0.81 | 55 | empty |
| 4 | 169 | 0.57 | 0.81 | 26 | empty |
| 5 | 125 | 0.54 | 0.82 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 561 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6JDK · Crystal structure of baeyer-villiger monooxygenase from parvibaculum lavamentivorans · the same entry in another collection · chain A against A, TM-score 1.00
- A7HU16 · AlphaFold monomer V2.0 prediction for baeyer-villiger monooxygenase (A7HU16) · a predicted model of the same protein · chain B 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 A7HU16
- Elsewhere: RCSB PDB 6JDK · PDBe 6JDK · UniProt A7HU16
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