Research workbench
Crystal structure of apo dicamba monooxygenase
Analyse Crystal structure of apo dicamba monooxygenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VSH
- Type
- protein
- Length
- 974 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dicamba O-demethylase, oxygenase component
- EC
- 1.14.15.-
- UniProt
- Q5S3I3
- Ligands
- FES
- Pockets
- 12 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dicamba O-demethylase, oxygenase component (EC 1.14.15.-) | protein | 332 | 25% helix, 32% strand | Q5S3I3 |
| B | Dicamba O-demethylase, oxygenase component (EC 1.14.15.-) | protein | 322 | 24% helix, 33% strand | Q5S3I3 |
| C | Dicamba O-demethylase, oxygenase component (EC 1.14.15.-) | protein | 320 | 27% helix, 32% strand | Q5S3I3 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 448 | 0.63 | 0.77 | 45 | empty |
| 2 | 270 | 0.60 | 0.79 | 28 | empty |
| 3 | 77 | 0.58 | 0.88 | 23 | empty |
| 4 | 248 | 0.58 | 0.79 | 29 | empty |
| 5 | 245 | 0.56 | 0.78 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1034 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 1008 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 966 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6VSH · Crystal structure of apo Dicamba Monooxygenase · the same entry in another collection · chain A against A, TM-score 1.00
- Q5S3I3 · AlphaFold monomer V2.0 prediction for dicamba O-demethylase, oxygenase component (Q5S3I3) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q5S3I3
- Elsewhere: RCSB PDB 6VSH · PDBe 6VSH · UniProt Q5S3I3
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