Research workbench
Crystal structure of dszb C27S mutant in complex with biphenyl-2- sulfinic acid
Analyse Crystal structure of dszb C27S mutant in complex with biphenyl-2- sulfinic acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DE4
- Type
- protein
- Length
- 691 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dibenzothiophene desulfurization enzyme B
- EC
- 3.13.1.3
- UniProt
- P54997
- Ligands
- BPS
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dibenzothiophene desulfurization enzyme B (EC 3.13.1.3) | protein | 344 | 51% helix, 17% strand | P54997 |
| B | Dibenzothiophene desulfurization enzyme B (EC 3.13.1.3) | protein | 347 | 51% helix, 17% strand | P54997 |
Ligands and binding sites
- BPS · 1,1'-biphenyl-2-sulfinic acid · ligand · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 101 | 0.78 | 0.98 | 30 | BPS |
| 2 | 109 | 0.78 | 0.97 | 31 | BPS |
| 3 | 195 | 0.62 | 0.83 | 31 | empty |
| 4 | 287 | 0.51 | 0.74 | 35 | empty |
| 5 | 52 | 0.37 | 0.80 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 271 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2DE4 · Crystal structure of DSZB C27S mutant in complex with biphenyl-2-sulfinic acid · the same entry in another collection · chain A against A, TM-score 1.00
- P54997 · AlphaFold monomer V2.0 prediction for 2'-hydroxybiphenyl-2-sulfinate desulfinase (P54997) · a predicted model of the same protein · 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 P54997
- Elsewhere: RCSB PDB 2DE4 · PDBe 2DE4 · UniProt P54997
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