Research workbench
Crystal structure of the phosphorybosylpyrophosphate synthetase II from thermus thermophilus
Analyse Crystal structure of the phosphorybosylpyrophosphate synthetase II from thermus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5T3O
- Type
- protein
- Length
- 921 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribose-phosphate pyrophosphokinase
- EC
- 2.7.6.1
- UniProt
- Q5SHU3
- Ligands
- ADP, SO4
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Ribose-phosphate pyrophosphokinase (EC 2.7.6.1) | protein | 307 | 33% helix, 23% strand | Q5SHU3 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 1189 | 0.69 | 0.74 | 130 | SO4 |
| 2 | 191 | 0.60 | 0.82 | 25 | ADP, SO4 |
| 3 | 124 | 0.56 | 0.84 | 34 | SO4 |
| 4 | 190 | 0.52 | 0.78 | 37 | SO4 |
| 5 | 101 | 0.48 | 0.81 | 21 | empty |
Interfaces
3 interfaces between chains.
- B–C · 347 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 309 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 308 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5T3O · Crystal structure of the Phosphorybosylpyrophosphate synthetase II from Thermus… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q5SHU3
- Elsewhere: RCSB PDB 5T3O · PDBe 5T3O · UniProt Q5SHU3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.