MolNFT v1 · #60818 · protein
How to switch off a histidine kinase: crystal structure of geobacillus stearothermophilus kinb with the inhibitor sda
3D36 · Sporulation kinase B: “How to switch off a histidine kinase: crystal structure of geobacillus stearothermophilus kinb with the…”. X-ray diffraction, 2 ligands (ADP, MG), 4 pockets (best druggability 0.80). MolNFT v1 #60818 on…
- PDB
- 3D36
- Type
- protein
- Length
- 480 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sporulation kinase B; Sporulation kinase inhibitor sda
- EC
- 2.7.13.3
- Ligands
- ADP, MG
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sporulation kinase B (EC 2.7.13.3) | protein | 217 | 46% helix, 24% strand | — |
| B | Sporulation kinase B (EC 2.7.13.3) | protein | 221 | 46% helix, 23% strand | — |
| C | Sporulation kinase inhibitor sda | protein | 42 | 69% helix, 0% strand | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 copies · chains B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 315 | 0.80 | 0.91 | 46 | MPD |
| 2 | 327 | 0.75 | 0.87 | 41 | ADP, MG |
| 3 | 533 | 0.74 | 0.82 | 64 | ADP, MG |
| 4 | 226 | 0.49 | 0.75 | 23 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1742 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 701 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3D36 · How to Switch Off a Histidine Kinase: Crystal Structure of Geobacillus stearothermophilus… · 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
- Elsewhere: RCSB PDB 3D36 · PDBe 3D36
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