MolNFT v1 · #126404 · protein
Crystal structure of hydroquinone 1,2-dioxygenase from sphingomonas sp. TTNP3
5M22 · Hydroquinone dioxygenase small subunit: “Crystal structure of hydroquinone 1,2-dioxygenase from sphingomonas sp. TTNP3”. X-ray diffraction, 1 ligand (FE), 20 pockets (best druggability 0.86). MolNFT v1 #126404 on GenesisL1: 3D…
- PDB
- 5M22
- Type
- protein
- Length
- 1,970 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
- FE
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 7 distinct chains · 15% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hydroquinone dioxygenase small subunit (EC 1.13.11.-) | protein | 166 | 11% helix, 49% strand | F8TW82 |
| B | Hydroquinone dioxygenase large subunit (EC 1.13.11.-) | protein | 325 | 17% helix, 36% strand | F8TW83 |
| D | Hydroquinone dioxygenase large subunit (EC 1.13.11.-) | protein | 325 | 17% helix, 36% strand | F8TW83 |
| E | Hydroquinone dioxygenase small subunit (EC 1.13.11.-) | protein | 167 | 10% helix, 46% 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 | 331 | 16% helix, 36% strand | F8TW83 |
Ligands and binding sites
- 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 948 | 0.86 | 0.88 | 81 | empty |
| 2 | 432 | 0.73 | 0.83 | 66 | empty |
| 3 | 361 | 0.70 | 0.82 | 44 | empty |
| 4 | 119 | 0.66 | 0.89 | 24 | empty |
| 5 | 111 | 0.59 | 0.86 | 30 | empty |
Interfaces
14 interfaces between chains.
- A–B · 2999 Ų buried · 50 hydrogen bonds · protein-protein
- C–D · 2897 Ų buried · 51 hydrogen bonds · protein-protein
- E–F · 2886 Ų buried · 53 hydrogen bonds · protein-protein
- G–H · 2814 Ų buried · 50 hydrogen bonds · protein-protein
- F–H · 1473 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5M22 · Crystal structure of hydroqui 1,2-dioxygenase from Sphingomonas sp. TTNP3 · 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 5M22 · PDBe 5M22 · UniProt F8TW82 · UniProt F8TW83
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