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Crystal structure of hydroquinone 1,2-dioxygenase from sphingomonas sp. TTNP3 in complex with 4-nitrophenol
Analyse Crystal structure of hydroquinone 1,2-dioxygenase from sphingomonas sp. TTNP3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5M4O
- Type
- protein
- Length
- 1,971 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydroquinone dioxygenase small subunit; Hydroquinone dioxygenase large subunit
- EC
- 1.13.11.-
- UniProt
- F8TW82, F8TW83
- Ligands
- NPO, FE
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 8 distinct chains · 15% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hydroquinone dioxygenase small subunit (EC 1.13.11.-) | protein | 166 | 10% helix, 46% strand | F8TW82 |
| B | Hydroquinone dioxygenase large subunit (EC 1.13.11.-) | protein | 325 | 17% helix, 36% strand | F8TW83 |
| C | Hydroquinone dioxygenase small subunit (EC 1.13.11.-) | protein | 167 | 11% helix, 48% strand | F8TW82 |
| D | Hydroquinone dioxygenase large subunit (EC 1.13.11.-) | protein | 324 | 17% helix, 36% strand | F8TW83 |
| E | Hydroquinone dioxygenase small subunit (EC 1.13.11.-) | protein | 167 | 10% helix, 45% strand | F8TW82 |
| F | Hydroquinone dioxygenase large subunit (EC 1.13.11.-) | protein | 326 | 17% helix, 36% strand | F8TW83 |
| G | Hydroquinone dioxygenase small subunit (EC 1.13.11.-) | protein | 164 | 11% helix, 48% strand | F8TW82 |
| H | Hydroquinone dioxygenase large subunit (EC 1.13.11.-) | protein | 332 | 17% helix, 36% strand | F8TW83 |
Ligands and binding sites
- NPO · P-nitrophenol · ligand · 4 copies · chains B, D, F, H
- FE · Fe (III) ion · metal · 4 copies · chains B, D, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 979 | 0.86 | 0.88 | 83 | empty |
| 2 | 930 | 0.80 | 0.82 | 95 | empty |
| 3 | 652 | 0.73 | 0.80 | 60 | empty |
| 4 | 393 | 0.56 | 0.74 | 42 | empty |
| 5 | 95 | 0.55 | 0.85 | 24 | empty |
Interfaces
14 interfaces between chains.
- C–D · 3014 Ų buried · 55 hydrogen bonds · protein-protein
- A–B · 2984 Ų buried · 52 hydrogen bonds · protein-protein
- E–F · 2839 Ų buried · 49 hydrogen bonds · protein-protein
- G–H · 2836 Ų buried · 54 hydrogen bonds · protein-protein
- F–H · 1472 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5M4O · Crystal structure of hydroqui 1,2-dioxygenase from Sphingomonas sp. TTNP3 in complex with… · 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 F8TW82
- Every structure of UniProt F8TW83
- Elsewhere: RCSB PDB 5M4O · PDBe 5M4O · UniProt F8TW82 · UniProt F8TW83
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