Research workbench
Crystal structure of the phosphoribosylpyrophosphate (prpp) synthetase from thermoplasma volcanium in complex with ADP-MG2+ and ribose 5- phosphate
Analyse Crystal structure of the phosphoribosylpyrophosphate (prpp) synthetase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MBI
- Type
- protein
- Length
- 1,144 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribose-phosphate pyrophosphokinase
- EC
- 2.7.6.1
- UniProt
- Q97CA5
- Ligands
- ADP, HSX, MG, PO4
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ribose-phosphate pyrophosphokinase (EC 2.7.6.1) | protein | 287 | 34% helix, 28% strand | Q97CA5 |
| C, D | Ribose-phosphate pyrophosphokinase (EC 2.7.6.1) | protein | 285 | 34% helix, 28% strand | Q97CA5 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, C, B, D
- HSX · 5-O-phosphono-alpha-D-ribofuranose · ligand · chains D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1076 | 0.73 | 0.76 | 101 | ADP, PO4, MG |
| 2 | 317 | 0.63 | 0.79 | 45 | HSX, MG, ADP |
| 3 | 286 | 0.61 | 0.80 | 43 | PO4, MG, ADP |
| 4 | 276 | 0.61 | 0.80 | 43 | PO4, MG, ADP |
| 5 | 187 | 0.48 | 0.76 | 24 | empty |
Interfaces
4 interfaces between chains.
- B–D · 2228 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 2226 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 375 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 234 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3MBI · Crystal structure of the phosphoribosylpyrophosphate (PRPP) synthetase from Thermoplasma… · the same entry in another collection · chain A against A, TM-score 1.00
- Q97CA5 · AlphaFold monomer V2.0 prediction for ribose-phosphate pyrophosphokinase (Q97CA5) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 Q97CA5
- Elsewhere: RCSB PDB 3MBI · PDBe 3MBI · UniProt Q97CA5
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