Research workbench
FT_T dioxygenase with bound dichlorprop
Analyse FT_T dioxygenase with bound dichlorprop in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D3H
- Type
- protein
- Length
- 1,145 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.03
- Source
- Sphingobium herbicidovorans
- Molecule
- FT_T dioxygenase
- Ligands
- FTV, AKG, CO, CL
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · resolution 2.03 · 2 distinct chains · 24% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, I | FT_T dioxygenase | protein | 286 | 24% helix, 28% strand | — |
| M | FT_T dioxygenase | protein | 287 | 24% helix, 28% strand | — |
Ligands and binding sites
- FTV · (2R)-2-(2,4-dichlorophenoxy)propanoic acid · ligand · 4 copies · chains A, B, I, M
- AKG · 2-oxoglutaric acid · ligand · 4 copies · chains A, B, I, M
- CO · Cobalt (II) ion · metal · 4 copies · chains A, B, I, M
- CL · Chloride ion · ion · 4 copies · chains A, B, I, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 212 | 0.81 | 0.94 | 38 | FTV, CO, AKG |
| 2 | 225 | 0.80 | 0.93 | 43 | FTV, CO, AKG |
| 3 | 186 | 0.78 | 0.93 | 29 | FTV, CO, AKG |
| 4 | 171 | 0.78 | 0.94 | 31 | FTV, CO, AKG |
| 5 | 291 | 0.61 | 0.79 | 28 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1058 Ų buried · 8 hydrogen bonds · protein-protein
- I–M · 1044 Ų buried · 10 hydrogen bonds · protein-protein
- B–M · 127 Ų buried · 1 hydrogen bond · protein-protein
- A–I · 126 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6D3H · FT_T dioxygenase with bound dichlorprop · 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
- Elsewhere: RCSB PDB 6D3H · PDBe 6D3H
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