MolNFT v1 · #34375 · protein
Crystal structure of dszb C27S mutant in complex with 2'- hydroxybiphenyl-2-sulfinic acid
2DE3 · Dibenzothiophene desulfurization enzyme B: “Crystal structure of dszb C27S mutant in complex with 2'- hydroxybiphenyl-2-sulfinic acid”. X-ray diffraction, 2 ligands (OBP, MG), 8 pockets (best druggability 0.79). MolNFT v1 #34375 on…
- PDB
- 2DE3
- 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
- OBP, MG
- Pockets
- 8 · best druggability 0.79
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 | 52% helix, 17% strand | P54997 |
Ligands and binding sites
- OBP · 2'-hydroxy-1,1'-biphenyl-2-sulfinic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains 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 | 117 | 0.79 | 0.97 | 31 | OBP |
| 2 | 120 | 0.79 | 0.97 | 32 | OBP |
| 3 | 180 | 0.62 | 0.84 | 23 | empty |
| 4 | 278 | 0.50 | 0.74 | 32 | empty |
| 5 | 82 | 0.36 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 265 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2DE3 · Crystal structure of DSZB C27S mutant in complex with 2'-hydroxybiphenyl-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 2DE3 · PDBe 2DE3 · UniProt P54997
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