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Crystal structure of the toluene 4-monooxygenase hydroxylase- ferredoxin C7S E16C C84A C85A variant electron-transfer complex
Analyse Crystal structure of the toluene 4-monooxygenase hydroxylase- ferredoxin C7S… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4P1B
- Type
- protein
- Length
- 1,976 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, Q00458
- Ligands
- FES, FE, NA
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 56% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Toluene-4-monooxygenase system protein a (EC 1.14.13.-) | protein | 490 | 66% helix, 4% strand | Q00456 |
| B, E | Toluene-4-monooxygenase system protein E (EC 1.14.13.-) | protein | 305 | 71% helix, 0% strand | Q00460 |
| C, F | Toluene-4-monooxygenase system protein B (EC 1.14.13.-) | protein | 82 | 16% helix, 38% strand | Q00457 |
| H, I | Toluene-4-monooxygenase system ferredoxin subunit | protein | 111 | 3% helix, 46% strand | Q00458 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains H, I
- FE · Fe (III) ion · metal · 4 copies · chains A, D
- NA · Sodium ion · metal · chains A
- ACT · Acetate ion · additive · 7 copies · chains A, I, B, D, H
- PEG · Di(hydroxyethyl)ether · additive · 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 783 | 0.78 | 0.82 | 112 | ACT |
| 2 | 209 | 0.72 | 0.88 | 36 | empty |
| 3 | 51 | 0.71 | 0.98 | 20 | empty |
| 4 | 53 | 0.69 | 0.97 | 20 | empty |
| 5 | 378 | 0.67 | 0.80 | 69 | empty |
Interfaces
12 interfaces between chains.
- D–E · 4357 Ų buried · 70 hydrogen bonds · protein-protein
- A–B · 4357 Ų buried · 67 hydrogen bonds · protein-protein
- A–C · 1313 Ų buried · 24 hydrogen bonds · protein-protein
- D–F · 1309 Ų buried · 24 hydrogen bonds · protein-protein
- A–I · 849 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4P1B · Crystal structure of the toluene 4-monooxygenase hydroxylase-ferredoxin C7S E16C C84A… · the same entry in another collection · chain I against I, 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 0.99
- Q00458 · AlphaFold monomer V2.0 prediction for toluene-4-monooxygenase system, ferredoxin… · a predicted model of the same protein · chain H against A, TM-score 0.99
- 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 Q00458
- Elsewhere: RCSB PDB 4P1B · PDBe 4P1B · UniProt Q00456 · UniProt Q00460 · UniProt Q00457 · UniProt Q00458
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