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The crystal structure of a diacylglycerol kinases from bacillus anthracis str. sterne
Analyse The crystal structure of a diacylglycerol kinases from bacillus anthracis str.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3S40
- Type
- protein
- Length
- 1,116 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diacylglycerol kinase
- UniProt
- Q81KC6
- Pockets
- 14 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diacylglycerol kinase | protein | 272 | 22% helix, 37% strand | Q81KC6 |
| B | Diacylglycerol kinase | protein | 293 | 27% helix, 33% strand | Q81KC6 |
| C | Diacylglycerol kinase | protein | 287 | 28% helix, 34% strand | Q81KC6 |
| D | Diacylglycerol kinase | protein | 264 | 24% helix, 37% strand | Q81KC6 |
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 761 | 0.70 | 0.77 | 90 | empty |
| 2 | 670 | 0.70 | 0.77 | 75 | empty |
| 3 | 492 | 0.63 | 0.76 | 57 | empty |
| 4 | 71 | 0.55 | 0.87 | 19 | empty |
| 5 | 67 | 0.49 | 0.84 | 24 | empty |
Interfaces
4 interfaces between chains.
- A–C · 908 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 853 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 818 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 796 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3S40 · The crystal structure of a diacylglycerol kinases from Bacillus anthracis str. Sterne · 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 Q81KC6
- Elsewhere: RCSB PDB 3S40 · PDBe 3S40 · UniProt Q81KC6
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