Research workbench
Crystal structure of toluene 2,3-dioxygenase
Analyse Crystal structure of toluene 2,3-dioxygenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EN1
- Type
- protein
- Length
- 604 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Benzene 1,2-dioxygenase subunit alpha; Benzene 1,2-dioxygenase subunit beta
- EC
- 1.14.12.11
- UniProt
- P0C618, P0C619
- Ligands
- FES, MBN, FE2
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Benzene 1,2-dioxygenase subunit alpha (EC 1.14.12.11) | protein | 424 | 33% helix, 25% strand | P0C618 |
| B | Benzene 1,2-dioxygenase subunit beta (EC 1.14.12.11) | protein | 180 | 26% helix, 39% strand | P0C619 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · chains A
- MBN · Toluene · ligand · chains A
- FE2 · Fe (II) ion · metal · 2 copies · chains A, B
- PE3 · 3,6,9,12,15,18,21,24,27,30,33,36,39-tridecaoxahentetracontane-1,41-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.74 | 0.99 | 17 | MBN |
| 2 | 321 | 0.68 | 0.82 | 37 | empty |
| 3 | 220 | 0.53 | 0.77 | 23 | empty |
| 4 | 65 | 0.43 | 0.81 | 21 | empty |
| 5 | 140 | 0.40 | 0.74 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1933 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 3EN1 · Crystal structure of Toluene 2,3-Dioxygenase · the same entry in another collection · chain A against A, TM-score 1.00
- P0C618 · AlphaFold monomer V2.0 prediction for benzene 1,2-dioxygenase subunit alpha (P0C618) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P0C619 · AlphaFold monomer V2.0 prediction for benzene 1,2-dioxygenase subunit beta (P0C619) · a predicted model of the same protein · chain B 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 P0C618
- Every structure of UniProt P0C619
- Elsewhere: RCSB PDB 3EN1 · PDBe 3EN1 · UniProt P0C618 · UniProt P0C619
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