MolNFT v1 · #134734 · protein
Toluene 4-monooxygenase (T4MOHD) bound to product after turnover in crystal
5TDU · Toluene-4-monooxygenase system protein a: “Toluene 4-monooxygenase (T4MOHD) bound to product after turnover in crystal”. X-ray diffraction, 2 ligands (PCR, FE), 9 pockets (best druggability 0.69). MolNFT v1 #134734 on GenesisL1: 3D…
- PDB
- 5TDU
- Type
- protein
- Length
- 980 residues
- Chains
- 4
- 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
- PCR, FE
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 60% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toluene-4-monooxygenase system protein a (EC 1.14.13.-) | protein | 490 | 67% helix, 3% strand | Q00456 |
| B | Toluene-4-monooxygenase system protein E (EC 1.14.13.-) | protein | 305 | 70% helix, 0% strand | Q00460 |
| C | Toluene-4-monooxygenase system protein B (EC 1.14.13.-) | protein | 83 | 17% helix, 39% strand | Q00457 |
| E | Toluene-4-monooxygenase system protein D (EC 1.14.13.-) | protein | 102 | 31% helix, 36% strand | Q00459 |
Ligands and binding sites
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 | 462 | 0.69 | 0.80 | 66 | empty |
| 2 | 159 | 0.63 | 0.85 | 21 | empty |
| 3 | 58 | 0.59 | 0.91 | 18 | empty |
| 4 | 135 | 0.46 | 0.77 | 23 | empty |
| 5 | 129 | 0.44 | 0.77 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 4354 Ų buried · 69 hydrogen bonds · protein-protein
- A–E · 1809 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 1327 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 5TDU · Toluene 4-monooxygenase (T4moHD) bound to product after turnover in crystal · the same entry in another collection · chain E against E, 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 0.98
- Q00459 · AlphaFold monomer V2.0 prediction for toluene-4-monooxygenase system, effector component… · a predicted model of the same protein · chain E against A, TM-score 0.93
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 5TDU · PDBe 5TDU · UniProt Q00456 · UniProt Q00460 · UniProt Q00457 · UniProt Q00459
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