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The crystal structure of sporulation kinase D sensor domain from bacillus subtilis subsp in complex with pyruvate at 2.0A resolution
Analyse The crystal structure of sporulation kinase D sensor domain from bacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JGP
- Type
- protein
- Length
- 412 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sporulation kinase D
- EC
- 2.7.13.3
- UniProt
- O31671
- Ligands
- PYR
- Pockets
- 3 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sporulation kinase D (EC 2.7.13.3) | protein | 206 | 37% helix, 28% strand | O31671 |
| B | Sporulation kinase D (EC 2.7.13.3) | protein | 206 | 36% helix, 27% strand | O31671 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 339 | 0.55 | 0.75 | 47 | empty |
| 2 | 167 | 0.43 | 0.74 | 31 | empty |
| 3 | 52 | 0.33 | 0.78 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1012 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 4JGP · The crystal structure of sporulation kinase D sensor domain from Bacillus subtilis subsp… · the same entry in another collection · chain A against A, TM-score 1.00
- O31671 · AlphaFold monomer V2.0 prediction for sporulation kinase D (O31671) · a predicted model of the same protein · chain B 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 O31671
- Elsewhere: RCSB PDB 4JGP · PDBe 4JGP · UniProt O31671
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