Research workbench
Toluene 4 monooxygenase hd complex with P-nitrophenol
Analyse Toluene 4 monooxygenase hd complex with P-nitrophenol in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3Q3N
- Type
- protein
- Length
- 981 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
- Q6Q8Q7, Q00460, Q00457, Q00459
- Ligands
- NPO, FE
- Pockets
- 12 · best druggability 0.73
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 | 491 | 67% helix, 3% strand | Q6Q8Q7 |
| 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 | 16% helix, 37% strand | Q00457 |
| E | Toluene-4-monooxygenase system protein D (EC 1.14.13.-) | protein | 102 | 31% helix, 36% strand | Q00459 |
Ligands and binding sites
- NPO · P-nitrophenol · ligand · 3 copies · chains A
- FE · Fe (III) ion · metal · 2 copies · chains A
- 1PE · Pentaethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.73 | 0.99 | 19 | FE, NPO |
| 2 | 58 | 0.73 | 0.98 | 24 | empty |
| 3 | 138 | 0.68 | 0.89 | 32 | empty |
| 4 | 136 | 0.62 | 0.86 | 19 | empty |
| 5 | 132 | 0.62 | 0.85 | 32 | NPO |
Interfaces
3 interfaces between chains.
- A–B · 4348 Ų buried · 67 hydrogen bonds · protein-protein
- A–E · 1816 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 1311 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 3Q3N · Toluene 4 monooxygenase HD complex with p-nitrophenol · the same entry in another collection · 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 B 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
- 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 Q6Q8Q7
- Every structure of UniProt Q00460
- Every structure of UniProt Q00457
- Every structure of UniProt Q00459
- Elsewhere: RCSB PDB 3Q3N · PDBe 3Q3N · UniProt Q6Q8Q7 · UniProt Q00460 · UniProt Q00457 · UniProt Q00459
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