MolNFT v1 · #139359 · protein
Crystal structure of tertiary complex of tdsc from paenibacillus sp. A11-2 with FMN and indole
5XDD · Thermophilic dibenzothiophene desulfurization enzyme C: “Crystal structure of tertiary complex of tdsc from paenibacillus sp. A11-2 with FMN and indole”. X-ray diffraction, 3 ligands (FMN, IND, SO4), 20 pockets (best druggability…
- PDB
- 5XDD
- Type
- protein
- Length
- 1,595 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, IND, SO4
- Pockets
- 20 · best druggability 0.91
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 | 400 | 59% helix, 11% strand | Q9LBX2 |
| B | Thermophilic dibenzothiophene desulfurization enzyme C | protein | 394 | 59% helix, 11% strand | Q9LBX2 |
| C | Thermophilic dibenzothiophene desulfurization enzyme C | protein | 401 | 58% helix, 11% strand | Q9LBX2 |
| D | Thermophilic dibenzothiophene desulfurization enzyme C | protein | 400 | 58% helix, 11% strand | Q9LBX2 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D
- IND · Indole · ligand · 2 copies · chains C, D
- SO4 · Sulfate ion · ion · 12 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1028 | 0.91 | 0.93 | 137 | FMN, IND |
| 2 | 867 | 0.90 | 0.92 | 128 | FMN, IND |
| 3 | 283 | 0.68 | 0.84 | 26 | empty |
| 4 | 123 | 0.66 | 0.89 | 22 | empty |
| 5 | 154 | 0.66 | 0.87 | 23 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2331 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 2067 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1817 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 1795 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 142 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5XDD · 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 5XDD · PDBe 5XDD · UniProt Q9LBX2
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