Research workbench
FT_T dioxygenase with bound quizalofop
Analyse FT_T dioxygenase with bound quizalofop in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D3M
- Type
- protein
- Length
- 1,143 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FT_T dioxygenase
- EC
- 1.14.11.44
- Ligands
- FTJ, AKG, CO, CL
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F, J | FT_T dioxygenase (EC 1.14.11.44) | protein | 286 | 24% helix, 28% strand | — |
| B | FT_T dioxygenase (EC 1.14.11.44) | protein | 285 | 24% helix, 29% strand | — |
Ligands and binding sites
- FTJ · (2R)-2-{4-[(6-chloroquinoxalin-2-yl) oxy]phenoxy}propanoic acid · ligand · 4 copies · chains A, B, F, J
- AKG · 2-oxoglutaric acid · ligand · 4 copies · chains A, B, F, J
- CO · Cobalt (II) ion · metal · 4 copies · chains A, B, F, J
- CL · Chloride ion · ion · 2 copies · chains A, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 248 | 0.78 | 0.91 | 46 | FTJ, AKG |
| 2 | 257 | 0.78 | 0.90 | 45 | CO, FTJ, AKG |
| 3 | 264 | 0.77 | 0.90 | 40 | FTJ, AKG |
| 4 | 241 | 0.75 | 0.89 | 34 | CO, FTJ, AKG |
| 5 | 280 | 0.60 | 0.79 | 28 | empty |
Interfaces
4 interfaces between chains.
- F–J · 1058 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1029 Ų buried · 10 hydrogen bonds · protein-protein
- A–J · 142 Ų buried · 3 hydrogen bonds · protein-protein
- B–F · 141 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6D3M · FT_T dioxygenase with bound quizalofop · 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 6D3M · PDBe 6D3M
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