MolNFT v1 · #4337 · protein
Crystal structures of bacillus subtilis phosphoribosylpyrophosphate synthetase: molecular basis of allosteric inhibition and activation.
1DKU · Protein (phosphoribosyl pyrophosphate synthetase): “Crystal structures of bacillus subtilis phosphoribosylpyrophosphate synthetase: molecular basis of allosteric…”. X-ray diffraction, 2 ligands (AP2, ABM), 5 pockets (best…
- PDB
- 1DKU
- Type
- protein
- Length
- 590 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (phosphoribosyl pyrophosphate synthetase)
- EC
- 2.7.6.1
- UniProt
- P14193
- Ligands
- AP2, ABM
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein (phosphoribosyl pyrophosphate synthetase) (EC 2.7.6.1) | protein | 295 | 35% helix, 25% strand | P14193 |
Ligands and binding sites
- AP2 · Phosphomethylphosphonic acid adenosyl ester · ligand · 2 copies · chains A, B
- ABM · Methyl phosphonic acid adenosine ester · ligand · 2 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 | 891 | 0.77 | 0.80 | 92 | AP2 |
| 2 | 70 | 0.30 | 0.74 | 19 | empty |
| 3 | 51 | 0.30 | 0.75 | 11 | empty |
| 4 | 64 | 0.29 | 0.73 | 19 | empty |
| 5 | 64 | 0.28 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1420 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 1DKU · 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 0.99
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 1DKU · PDBe 1DKU · UniProt P14193
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