Research workbench
Crystal structure of yggs from fusobacterium nucleatum
Analyse Crystal structure of yggs from fusobacterium nucleatum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7F8E
- Type
- protein
- Length
- 665 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxal phosphate homeostasis protein
- UniProt
- Q8RFW9
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Pyridoxal phosphate homeostasis protein | protein | 223 | 45% helix, 19% strand | Q8RFW9 |
| B | Pyridoxal phosphate homeostasis protein | protein | 219 | 46% helix, 18% strand | Q8RFW9 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 221 | 0.55 | 0.78 | 37 | SO4 |
| 2 | 136 | 0.46 | 0.77 | 26 | SO4 |
| 3 | 100 | 0.45 | 0.79 | 21 | empty |
| 4 | 122 | 0.44 | 0.78 | 24 | empty |
| 5 | 80 | 0.43 | 0.80 | 20 | empty |
Interfaces
2 interfaces between chains.
- A–C · 599 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 533 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 modified (engineered).
Compared structures
- 7F8E · Crystal structure of YggS from Fusobacterium nucleatum · 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 Q8RFW9
- Elsewhere: RCSB PDB 7F8E · PDBe 7F8E · UniProt Q8RFW9
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