MolNFT v1 · #139293 · protein
Crystal structure of dibenzothiophene monooxygenase (tdsc) from paenibacillus sp. A11-2
5XB8 · Thermophilic dibenzothiophene desulfurization enzyme C: “Crystal structure of dibenzothiophene monooxygenase (tdsc) from paenibacillus sp. A11-2”. X-ray diffraction, 1 ligand (SO4), 16 pockets (best druggability 0.84). MolNFT v1…
- PDB
- 5XB8
- Type
- protein
- Length
- 1,553 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thermophilic dibenzothiophene desulfurization enzyme C
- UniProt
- Q9LBX2
- Ligands
- SO4
- Pockets
- 16 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 59% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thermophilic dibenzothiophene desulfurization enzyme C | protein | 389 | 60% helix, 11% strand | Q9LBX2 |
| B | Thermophilic dibenzothiophene desulfurization enzyme C | protein | 388 | 60% helix, 11% strand | Q9LBX2 |
| C | Thermophilic dibenzothiophene desulfurization enzyme C | protein | 388 | 60% helix, 11% strand | Q9LBX2 |
| D | Thermophilic dibenzothiophene desulfurization enzyme C | protein | 388 | 59% helix, 11% strand | Q9LBX2 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 727 | 0.84 | 0.88 | 104 | empty |
| 2 | 447 | 0.82 | 0.89 | 70 | empty |
| 3 | 276 | 0.75 | 0.88 | 36 | empty |
| 4 | 218 | 0.74 | 0.89 | 34 | empty |
| 5 | 196 | 0.72 | 0.88 | 29 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1762 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 1760 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1607 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1600 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 143 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5XB8 · Crystal structure of dibenzothiophene monooxygenase (TdsC) from Paenibacillus sp. A11-2 · 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 Q9LBX2
- Elsewhere: RCSB PDB 5XB8 · PDBe 5XB8 · UniProt Q9LBX2
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