Research workbench
Crystal structure of the sulfite dehydrogenase, sort R78K mutant from sinorhizobium meliloti
Analyse Crystal structure of the sulfite dehydrogenase, sort R78K mutant from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K3X
- Type
- protein
- Length
- 688 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative sulfite oxidase
- EC
- 1.8.3.1
- UniProt
- Q92M24
- Ligands
- MSS
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative sulfite oxidase (EC 1.8.3.1) | protein | 343 | 12% helix, 35% strand | Q92M24 |
| B | Putative sulfite oxidase (EC 1.8.3.1) | protein | 345 | 13% helix, 36% strand | Q92M24 |
Ligands and binding sites
- MSS · (molybdopterin-S,S)-oxo-molybdenum · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 83 | 0.75 | 0.98 | 21 | MSS |
| 2 | 76 | 0.74 | 0.97 | 23 | MSS |
| 3 | 359 | 0.65 | 0.79 | 38 | empty |
| 4 | 346 | 0.64 | 0.79 | 35 | empty |
| 5 | 120 | 0.47 | 0.79 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1271 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 5K3X · Crystal Structure of the sulfite dehydrogenase, SorT R78K mutant from Sinorhizobium… · 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 Q92M24
- Elsewhere: RCSB PDB 5K3X · PDBe 5K3X · UniProt Q92M24
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