Research workbench
Oxygenated toluene intermediate in toluene 4-monooxygenase (T4MOHD) after reaction in the crystal
Analyse Oxygenated toluene intermediate in toluene 4-monooxygenase (T4MOHD) after… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TDT
- Type
- protein
- Length
- 1,957 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toluene-4-monooxygenase system protein a; Toluene-4-monooxygenase system protein E…
- EC
- 1.14.13.-
- UniProt
- Q00456, Q00460, Q00457, Q00459
- Ligands
- MBN, FE, PER
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 7 distinct chains · 62% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toluene-4-monooxygenase system protein a (EC 1.14.13.-) | protein | 489 | 67% helix, 3% strand | Q00456 |
| B | Toluene-4-monooxygenase system protein E (EC 1.14.13.-) | protein | 306 | 69% helix, 0% strand | Q00460 |
| C, G | Toluene-4-monooxygenase system protein B (EC 1.14.13.-) | protein | 82 | 17% helix, 39% strand | Q00457 |
| D | Toluene-4-monooxygenase system protein a (EC 1.14.13.-) | protein | 490 | 69% helix, 3% strand | Q00456 |
| E | Toluene-4-monooxygenase system protein D (EC 1.14.13.-) | protein | 102 | 31% helix, 36% strand | Q00459 |
| F | Toluene-4-monooxygenase system protein E (EC 1.14.13.-) | protein | 305 | 71% helix, 0% strand | Q00460 |
| H | Toluene-4-monooxygenase system protein D (EC 1.14.13.-) | protein | 101 | 31% helix, 37% strand | Q00459 |
Ligands and binding sites
- MBN · Toluene · ligand · 5 copies · chains A, C, D, G
- FE · Fe (III) ion · metal · 4 copies · chains A, D
- PER · Peroxide ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1002 | 0.88 | 0.89 | 110 | empty |
| 2 | 75 | 0.75 | 0.97 | 24 | MBN |
| 3 | 53 | 0.73 | 0.99 | 19 | FE |
| 4 | 131 | 0.71 | 0.90 | 33 | MBN |
| 5 | 289 | 0.69 | 0.84 | 60 | empty |
Interfaces
14 interfaces between chains.
- A–B · 4375 Ų buried · 70 hydrogen bonds · protein-protein
- D–F · 4339 Ų buried · 69 hydrogen bonds · protein-protein
- D–H · 1783 Ų buried · 31 hydrogen bonds · protein-protein
- A–E · 1779 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 1328 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 5TDT · Oxygenated toluene intermediate in toluene 4-monooxygenase (T4moHD) after reaction in the… · the same entry in another collection · chain H against H, TM-score 1.00
- Q00456 · AlphaFold monomer V2.0 prediction for toluene-4-monooxygenase system, hydroxylase… · a predicted model of the same protein · chain A against A, TM-score 1.00
- Q00460 · AlphaFold monomer V2.0 prediction for toluene-4-monooxygenase system, hydroxylase… · a predicted model of the same protein · chain F 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 Q00456
- Every structure of UniProt Q00460
- Every structure of UniProt Q00457
- Every structure of UniProt Q00459
- Elsewhere: RCSB PDB 5TDT · PDBe 5TDT · UniProt Q00456 · UniProt Q00460 · UniProt Q00457 · UniProt Q00459
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