Research workbench
Crystal structure of dibenzothiophene sulfone monooxygenase bdsa in complex with FMN at 2.4 ångström
Analyse Crystal structure of dibenzothiophene sulfone monooxygenase bdsa in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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