MolNFT v1 · #139590 · protein
Crystal structure of dibenzothiophene sulfone monooxygenase bdsa in complex with FMN at 2.4 ångström
5XKD · Dibenzothiophene desulfurization enzyme a: “Crystal structure of dibenzothiophene sulfone monooxygenase bdsa in complex with FMN at 2.4 ångström”. X-ray diffraction, 1 ligand (FMN), 16 pockets (best druggability 0.82). MolNFT v1…
- PDB
- 5XKD
- Type
- protein
- Length
- 1,780 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dibenzothiophene desulfurization enzyme a
- EC
- 1.14.14.22
- UniProt
- Q8GRC7
- Ligands
- FMN
- Pockets
- 16 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Dibenzothiophene desulfurization enzyme a (EC 1.14.14.22) | protein | 445 | 44% helix, 15% strand | Q8GRC7 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 625 | 0.82 | 0.87 | 68 | empty |
| 2 | 922 | 0.79 | 0.81 | 77 | FMN |
| 3 | 947 | 0.77 | 0.79 | 90 | FMN |
| 4 | 866 | 0.77 | 0.80 | 63 | FMN |
| 5 | 833 | 0.75 | 0.79 | 67 | FMN |
Interfaces
6 interfaces between chains.
- C–D · 3272 Ų buried · 57 hydrogen bonds · protein-protein
- A–B · 3202 Ų buried · 57 hydrogen bonds · protein-protein
- A–C · 972 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 945 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 90 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5XKD · Crystal structure of dibenzothiophene sulfone monooxygenase BdsA in complex with FMN at… · 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 Q8GRC7
- Elsewhere: RCSB PDB 5XKD · PDBe 5XKD · UniProt Q8GRC7
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