MolNFT v1 · #139362 · protein
Crystal structure of tertiary complex of tdsc from paenibacillus sp. A11-2 with FMN and dibenzothiophene sulfoxide
5XDG · Thermophilic dibenzothiophene desulfurization enzyme C: “Crystal structure of tertiary complex of tdsc from paenibacillus sp. A11-2 with FMN and dibenzothiophene…”. X-ray diffraction, 3 ligands (FMN, 83U, SO4), 20 pockets (best…
- PDB
- 5XDG
- Type
- protein
- Length
- 1,600 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thermophilic dibenzothiophene desulfurization enzyme C
- UniProt
- Q9LBX2
- Ligands
- FMN, 83U, SO4
- Pockets
- 20 · best druggability 0.91
Structure
x-ray diffraction · 1 distinct chain · 59% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Thermophilic dibenzothiophene desulfurization enzyme C | protein | 400 | 59% helix, 11% strand | Q9LBX2 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D
- 83U · dibenzothiophene 5-oxide · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1056 | 0.91 | 0.92 | 137 | FMN, 83U |
| 2 | 1142 | 0.90 | 0.92 | 128 | FMN, 83U |
| 3 | 228 | 0.71 | 0.87 | 32 | empty |
| 4 | 328 | 0.66 | 0.81 | 41 | empty |
| 5 | 141 | 0.65 | 0.87 | 22 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2363 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 2305 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 1819 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1803 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 143 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5XDG · Crystal structure of tertiary complex of TdsC from Paenibacillus sp. A11-2 with FMN and… · 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 5XDG · PDBe 5XDG · UniProt Q9LBX2
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