MolNFT v1 · #134735 · protein
Intermediate O2 diiron complex in the Q228A variant of toluene 4- moonoxygenase (T4MOHD)
5TDV · Toluene-4-monooxygenase system protein a: “Intermediate O2 diiron complex in the Q228A variant of toluene 4- moonoxygenase (T4MOHD)”. X-ray diffraction, 2 ligands (FE, PER), 20 pockets (best druggability 0.87). MolNFT v1 #134735 on…
- PDB
- 5TDV
- Type
- protein
- Length
- 1,959 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
- FE, PER
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 6 distinct chains · 60% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Toluene-4-monooxygenase system protein a (EC 1.14.13.-) | protein | 491 | 67% helix, 3% strand | Q00456 |
| B | Toluene-4-monooxygenase system protein E (EC 1.14.13.-) | protein | 305 | 71% helix, 0% strand | Q00460 |
| C, G | Toluene-4-monooxygenase system protein B (EC 1.14.13.-) | protein | 82 | 17% helix, 37% strand | Q00457 |
| E | Toluene-4-monooxygenase system protein D (EC 1.14.13.-) | protein | 101 | 31% helix, 37% 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 | 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
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 937 | 0.87 | 0.89 | 112 | empty |
| 2 | 59 | 0.75 | 0.99 | 18 | empty |
| 3 | 138 | 0.71 | 0.91 | 33 | empty |
| 4 | 159 | 0.70 | 0.89 | 39 | empty |
| 5 | 79 | 0.66 | 0.92 | 20 | empty |
Interfaces
14 interfaces between chains.
- D–F · 4366 Ų buried · 69 hydrogen bonds · protein-protein
- A–B · 4324 Ų buried · 67 hydrogen bonds · protein-protein
- D–H · 1804 Ų buried · 35 hydrogen bonds · protein-protein
- A–E · 1795 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 1325 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 5TDV · Intermediate O2 diiron complex in the Q228A variant of Toluene 4-moonoxygenase (T4moHD) · the same entry in another collection · chain H against H, 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 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
- Every structure of UniProt Q00459
- Elsewhere: RCSB PDB 5TDV · PDBe 5TDV · UniProt Q00456 · UniProt Q00460 · UniProt Q00457 · UniProt Q00459
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