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Structural genomics, the crystal structure of spovg from bacillus subtilis subsp. subtilis str. 168
Analyse Structural genomics, the crystal structure of spovg from bacillus subtilis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IA9
- Type
- protein
- Length
- 548 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative septation protein spovg
- UniProt
- P28015
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.63
Structure
x-ray diffraction · 6 distinct chains · 25% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative septation protein spovg | protein | 94 | 27% helix, 45% strand | P28015 |
| B | Putative septation protein spovg | protein | 95 | 28% helix, 41% strand | P28015 |
| C | Putative septation protein spovg | protein | 86 | 21% helix, 47% strand | P28015 |
| D | Putative septation protein spovg | protein | 99 | 31% helix, 41% strand | P28015 |
| E | Putative septation protein spovg | protein | 84 | 18% helix, 45% strand | P28015 |
| F | Putative septation protein spovg | protein | 90 | 26% helix, 40% strand | P28015 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, D, E
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 382 | 0.63 | 0.78 | 49 | empty |
| 2 | 279 | 0.54 | 0.75 | 37 | SO4 |
| 3 | 190 | 0.52 | 0.78 | 26 | empty |
| 4 | 163 | 0.49 | 0.77 | 25 | empty |
| 5 | 124 | 0.47 | 0.79 | 27 | empty |
Interfaces
8 interfaces between chains.
- C–D · 1229 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 1223 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1119 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 687 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 647 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 2IA9 · Structural Genomics, the crystal structure of SpoVG from Bacillus subtilis subsp.… · the same entry in another collection · chain F against F, TM-score 1.00
- P28015 · AlphaFold monomer V2.0 prediction for putative septation protein spovg (P28015) · a predicted model of the same protein · chain C against A, TM-score 0.91
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 P28015
- Elsewhere: RCSB PDB 2IA9 · PDBe 2IA9 · UniProt P28015
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