MolNFT v1 · #65324 · protein
Crystal structure of dicamba monooxygenase with non-heme iron and dicamba
3GTS · Ddmc: “Crystal structure of dicamba monooxygenase with non-heme iron and dicamba”. X-ray diffraction, 3 ligands (FES, D3M, FE), 10 pockets (best druggability 0.83). MolNFT v1 #65324 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3GTS
- Type
- protein
- Length
- 1,009 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ddmc
- UniProt
- Q5S3I3
- Ligands
- FES, D3M, FE
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ddmc | protein | 341 | 30% helix, 33% strand | Q5S3I3 |
| C | Ddmc | protein | 327 | 25% helix, 31% strand | Q5S3I3 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 3 copies · chains A, B, C
- D3M · 3,6-dichloro-2-methoxybenzoic acid · ligand · 2 copies · chains A, B
- FE · Fe (III) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 214 | 0.83 | 0.96 | 41 | D3M |
| 2 | 191 | 0.82 | 0.96 | 39 | FE, D3M |
| 3 | 517 | 0.70 | 0.80 | 56 | empty |
| 4 | 273 | 0.60 | 0.79 | 27 | empty |
| 5 | 254 | 0.57 | 0.78 | 27 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1172 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1162 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1021 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3GTS · Crystal Structure of Dicamba Monooxygenase with Non-heme Iron and Dicamba · 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 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 Q5S3I3
- Elsewhere: RCSB PDB 3GTS · PDBe 3GTS · UniProt Q5S3I3
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