Research workbench
Crystal structures of bacillus subtilis phosphoribosylpyrophosphate synthetase: molecular basis of allosteric inhibition and activation.
Analyse Crystal structures of bacillus subtilis phosphoribosylpyrophosphate synthetase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DKR
- Type
- protein
- Length
- 604 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoribosyl pyrophosphate synthetase
- EC
- 2.7.6.1
- UniProt
- P14193
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoribosyl pyrophosphate synthetase (EC 2.7.6.1) | protein | 298 | 34% helix, 25% strand | P14193 |
| B | Phosphoribosyl pyrophosphate synthetase (EC 2.7.6.1) | protein | 306 | 32% helix, 25% strand | P14193 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 939 | 0.77 | 0.80 | 85 | SO4 |
| 2 | 170 | 0.46 | 0.76 | 35 | empty |
| 3 | 119 | 0.40 | 0.75 | 24 | empty |
| 4 | 71 | 0.29 | 0.73 | 17 | empty |
| 5 | 50 | 0.27 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1381 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 1DKR · Crystal structures of bacillus subtilis phosphoribosylpyrophosphate synthetase: molecular… · the same entry in another collection · chain A against A, TM-score 1.00
- P14193 · AlphaFold monomer V2.0 prediction for ribose-phosphate pyrophosphokinase (P14193) · a predicted model of the same protein · chain A 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 P14193
- Elsewhere: RCSB PDB 1DKR · PDBe 1DKR · UniProt P14193
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