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Crystal structure of SufU from Bacillus subtilis with Cys persulfurated
Analyse Crystal structure of SufU from Bacillus subtilis with Cys persulfurated in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JZW
- Type
- protein
- Length
- 554 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.64
- Source
- Bacillus subtilis (strain 168)
- Molecule
- Zinc-dependent sulfurtransferase SufU
- EC
- 2.-.-.-
- UniProt
- O32163
- Ligands
- ZN
- Pockets
- 8 · best druggability 0.39
Structure
x-ray diffraction · resolution 2.64 · 3 distinct chains · 55% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Zinc-dependent sulfurtransferase SufU (EC 2.-.-.-) | protein | 142 | 54% helix, 21% strand | O32163 |
| B | Zinc-dependent sulfurtransferase SufU (EC 2.-.-.-) | protein | 138 | 54% helix, 22% strand | O32163 |
| D | Zinc-dependent sulfurtransferase SufU (EC 2.-.-.-) | protein | 132 | 57% helix, 23% strand | O32163 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.39 | 0.77 | 17 | empty |
| 2 | 89 | 0.38 | 0.76 | 17 | empty |
| 3 | 75 | 0.37 | 0.77 | 15 | empty |
| 4 | 70 | 0.37 | 0.78 | 16 | empty |
| 5 | 63 | 0.36 | 0.78 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–D · 477 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 467 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 6JZW · Crystal structure of sufu from bacillus subtilis with cys persulfurated · the same entry in another collection · chain A against A, TM-score 1.00
- O32163 · AlphaFold monomer V2.0 prediction for zinc-dependent sulfurtransferase sufu (O32163) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 O32163
- Elsewhere: RCSB PDB 6JZW · PDBe 6JZW · UniProt O32163
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