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Crystal structure of the small alarmone synthetase 1 from bacillus subtilis
Analyse Crystal structure of the small alarmone synthetase 1 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
- 5DEC
- Type
- protein
- Length
- 751 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTP pyrophosphokinase yjbm
- EC
- 2.7.6.5
- UniProt
- O31611
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTP pyrophosphokinase yjbm (EC 2.7.6.5) | protein | 188 | 54% helix, 23% strand | O31611 |
| B | GTP pyrophosphokinase yjbm (EC 2.7.6.5) | protein | 191 | 52% helix, 23% strand | O31611 |
| C | GTP pyrophosphokinase yjbm (EC 2.7.6.5) | protein | 183 | 55% helix, 23% strand | O31611 |
| D | GTP pyrophosphokinase yjbm (EC 2.7.6.5) | protein | 189 | 52% helix, 23% strand | O31611 |
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 859 | 0.75 | 0.79 | 93 | empty |
| 2 | 1156 | 0.73 | 0.76 | 97 | empty |
| 3 | 162 | 0.54 | 0.80 | 18 | empty |
| 4 | 211 | 0.53 | 0.77 | 19 | empty |
| 5 | 84 | 0.47 | 0.81 | 20 | empty |
Interfaces
4 interfaces between chains.
- A–D · 1444 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1375 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 1016 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 897 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5DEC · Crystal structure of the small alarmone synthetase 1 from Bacillus subtilis · the same entry in another collection · chain D against D, TM-score 1.00
- O31611 · AlphaFold monomer V2.0 prediction for GTP pyrophosphokinase yjbm (O31611) · 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 O31611
- Elsewhere: RCSB PDB 5DEC · PDBe 5DEC · UniProt O31611
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