MolNFT v1 · #77694 · protein
Toluene 4 monooxygenase H with 4-bromophenol
3RMK · Toluene-4-monooxygenase system protein a: “Toluene 4 monooxygenase H with 4-bromophenol”. X-ray diffraction, 3 ligands (BML, CA, FE), 20 pockets (best druggability 0.82). MolNFT v1 #77694 on GenesisL1: 3D structure, binding sites…
- PDB
- 3RMK
- Type
- protein
- Length
- 1,757 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
- BML, CA, FE
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 63% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toluene-4-monooxygenase system protein a (EC 1.14.13.-) | protein | 492 | 66% helix, 3% strand | Q00456 |
| B | Toluene-4-monooxygenase system protein E (EC 1.14.13.-) | protein | 304 | 70% helix, 0% strand | Q00460 |
| C | Toluene-4-monooxygenase system protein B (EC 1.14.13.-) | protein | 81 | 17% helix, 37% strand | Q00457 |
| D | Toluene-4-monooxygenase system protein a (EC 1.14.13.-) | protein | 491 | 65% helix, 3% strand | Q00456 |
| E | Toluene-4-monooxygenase system protein E (EC 1.14.13.-) | protein | 306 | 69% helix, 0% strand | Q00460 |
| F | Toluene-4-monooxygenase system protein B (EC 1.14.13.-) | protein | 83 | 17% helix, 39% strand | Q00457 |
Ligands and binding sites
- BML · 4-bromophenol · ligand · 9 copies · chains A, C, B, D, F
- CA · Calcium ion · metal · 16 copies · chains A, B, E, D, F
- FE · Fe (III) ion · metal · 4 copies · chains A, D
- PGE · Triethylene glycol · additive · 2 copies · chains E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 409 | 0.82 | 0.90 | 58 | BML |
| 2 | 889 | 0.81 | 0.83 | 78 | empty |
| 3 | 610 | 0.80 | 0.85 | 61 | BML |
| 4 | 775 | 0.79 | 0.83 | 64 | CA |
| 5 | 176 | 0.74 | 0.90 | 37 | BML |
Interfaces
6 interfaces between chains.
- D–E · 4358 Ų buried · 65 hydrogen bonds · protein-protein
- A–B · 4347 Ų buried · 69 hydrogen bonds · protein-protein
- A–C · 1357 Ų buried · 26 hydrogen bonds · protein-protein
- D–F · 1346 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 868 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3RMK · Toluene 4 monooxygenase H with 4-bromophenol · 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 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
- Elsewhere: RCSB PDB 3RMK · PDBe 3RMK · UniProt Q00456 · UniProt Q00460 · UniProt Q00457
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