Research workbench
Toluene bound in the resting active site of toluene 4-monooxygenase (T4MOH)
Analyse Toluene bound in the resting active site of toluene 4-monooxygenase (T4MOH) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TDS
- Type
- protein
- Length
- 1,750 residues
- Chains
- 6
- 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
- Ligands
- MBN, MG, FE, CL
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 62% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Toluene-4-monooxygenase system protein a (EC 1.14.13.-) | protein | 490 | 68% helix, 3% strand | Q00456 |
| B | Toluene-4-monooxygenase system protein E (EC 1.14.13.-) | protein | 301 | 70% helix, 0% strand | Q00460 |
| C | Toluene-4-monooxygenase system protein B (EC 1.14.13.-) | protein | 82 | 17% helix, 39% strand | Q00457 |
| E | Toluene-4-monooxygenase system protein E (EC 1.14.13.-) | protein | 304 | 70% helix, 0% strand | Q00460 |
| F | Toluene-4-monooxygenase system protein B (EC 1.14.13.-) | protein | 83 | 17% helix, 37% strand | Q00457 |
Ligands and binding sites
- MBN · Toluene · ligand · 9 copies · chains A, C, B, D, F
- MG · Magnesium ion · metal · 9 copies · chains A, B, E, C, D, F
- FE · Fe (III) ion · metal · 4 copies · chains A, D
- CL · Chloride ion · ion · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 361 | 0.82 | 0.91 | 59 | MBN |
| 2 | 939 | 0.82 | 0.83 | 87 | empty |
| 3 | 856 | 0.80 | 0.83 | 73 | MG |
| 4 | 634 | 0.79 | 0.84 | 75 | MBN |
| 5 | 72 | 0.76 | 0.99 | 23 | MBN |
Interfaces
6 interfaces between chains.
- D–E · 4408 Ų buried · 65 hydrogen bonds · protein-protein
- A–B · 4398 Ų buried · 65 hydrogen bonds · protein-protein
- D–F · 1353 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1332 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 854 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5TDS · Toluene bound in the resting active site of toluene 4-monooxygenase (T4moH) · the same entry in another collection · chain F against F, TM-score 1.00
- Q00460 · AlphaFold monomer V2.0 prediction for toluene-4-monooxygenase system, hydroxylase… · a predicted model of the same protein · chain B against A, 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
- Q00457 · AlphaFold monomer V2.0 prediction for toluene-4-monooxygenase system, hydroxylase… · a predicted model of the same protein · chain C 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
- Elsewhere: RCSB PDB 5TDS · PDBe 5TDS · UniProt Q00456 · UniProt Q00460 · UniProt Q00457
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