Research workbench
Complex between the reductase and ferredoxin components of toluene dioxygenase
Analyse Complex between the reductase and ferredoxin components of toluene dioxygenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EMJ
- Type
- protein
- Length
- 512 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toda; Toluene 1,2-dioxygenase system ferredoxin subunit
- UniProt
- Q7BPB6, P0C620
- Ligands
- FAD, FES
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toda | protein | 406 | 27% helix, 30% strand | Q7BPB6 |
| B | Toluene 1,2-dioxygenase system ferredoxin subunit | protein | 106 | 6% helix, 45% strand | P0C620 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- FES · Fe2/s2 (inorganic) cluster · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 901 | 0.81 | 0.83 | 85 | FAD |
| 2 | 187 | 0.54 | 0.79 | 29 | empty |
| 3 | 209 | 0.51 | 0.76 | 30 | empty |
| 4 | 53 | 0.43 | 0.83 | 15 | empty |
| 5 | 68 | 0.42 | 0.81 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 796 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4EMJ · Complex between the reductase and ferredoxin components of toluene dioxygenase · the same entry in another collection · chain A against A, TM-score 1.00
- P0C620 · AlphaFold monomer V2.0 prediction for toluene 1,2-dioxygenase system ferredoxin subunit… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q7BPB6
- Every structure of UniProt P0C620
- Elsewhere: RCSB PDB 4EMJ · PDBe 4EMJ · UniProt Q7BPB6 · UniProt P0C620
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