Research workbench
X-ray crystal structure of TOLUENE/O-xylene monooxygenase hydroxylase I100W mutant
Analyse X-ray crystal structure of TOLUENE/O-xylene monooxygenase hydroxylase I100W… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2RDB
- Type
- protein
- Length
- 896 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Toluene, O-xylene monooxygenase oxygenase subunit
- UniProt
- O87798, O87802, O87799
- Ligands
- FE
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 63% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Toluene, O-xylene monooxygenase oxygenase subunit | protein | 491 | 66% helix, 2% strand | O87798 |
| B | Toluene, O-xylene monooxygenase oxygenase subunit | protein | 322 | 72% helix, 0% strand | O87802 |
| C | Toluene, O-xylene monooxygenase oxygenase subunit | protein | 83 | 14% helix, 39% strand | O87799 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 2 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains A
- P6G · Hexaethylene glycol · additive · chains A, B
- MPO · 3[N-morpholino]propane sulfonic acid · additive · chains 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.75 | 0.99 | 17 | GOL |
| 2 | 117 | 0.73 | 0.93 | 21 | empty |
| 3 | 120 | 0.68 | 0.90 | 31 | GOL |
| 4 | 89 | 0.54 | 0.85 | 28 | empty |
| 5 | 64 | 0.47 | 0.83 | 13 | empty |
Interfaces
2 interfaces between chains.
- A–B · 4246 Ų buried · 72 hydrogen bonds · protein-protein
- A–C · 1442 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 2RDB · X-ray Crystal Structure of Toluene/o-Xylene Monooxygenase Hydroxylase I100W Mutant · the same entry in another collection · chain A against A, TM-score 1.00
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 O87798
- Every structure of UniProt O87802
- Every structure of UniProt O87799
- Elsewhere: RCSB PDB 2RDB · PDBe 2RDB · UniProt O87798 · UniProt O87802 · UniProt O87799
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