Research workbench
2.0A crystal structure of human phosphoribosyl pyrophosphate synthetase 1
Analyse 2.0A crystal structure of human phosphoribosyl pyrophosphate synthetase 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3S5J
- Type
- protein
- Length
- 612 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribose-phosphate pyrophosphokinase 1
- EC
- 2.7.6.1
- UniProt
- P60891
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Ribose-phosphate pyrophosphokinase 1 (EC 2.7.6.1) | protein | 308 | 37% helix, 25% strand | P60891 |
| A | Ribose-phosphate pyrophosphokinase 1 (EC 2.7.6.1) | protein | 304 | 36% helix, 25% strand | P60891 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 196 | 0.70 | 0.87 | 33 | empty |
| 2 | 184 | 0.68 | 0.87 | 33 | empty |
| 3 | 217 | 0.56 | 0.79 | 34 | SO4 |
| 4 | 143 | 0.55 | 0.82 | 22 | empty |
| 5 | 258 | 0.50 | 0.75 | 39 | SO4 |
Interfaces
1 interface between chains.
- B–A · 2010 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 3S5J · 2.0A Crystal structure of human phosphoribosyl pyrophosphate synthetase 1 · the same entry in another collection · chain B against B, TM-score 1.00
- P60891 · AlphaFold monomer V2.0 prediction for ribose-phosphate pyrophosphokinase 1 (P60891) · a predicted model of the same protein · chain B 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 P60891
- Elsewhere: RCSB PDB 3S5J · PDBe 3S5J · UniProt P60891
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