Research workbench
Crystal structure of the phosphorybosylpyrophosphate synthetase II from thermus thermophilus at R32 space group
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
- 7PN0
- Type
- protein
- Length
- 620 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribose-phosphate pyrophosphokinase
- EC
- 2.7.6.1
- UniProt
- A0A7G5B4V6
- Ligands
- ADP, SO4
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribose-phosphate pyrophosphokinase (EC 2.7.6.1) | protein | 312 | 36% helix, 27% strand | A0A7G5B4V6 |
| B | Ribose-phosphate pyrophosphokinase (EC 2.7.6.1) | protein | 308 | 33% helix, 25% strand | A0A7G5B4V6 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 8 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1093 | 0.79 | 0.81 | 108 | SO4, ADP |
| 2 | 258 | 0.62 | 0.81 | 40 | SO4 |
| 3 | 80 | 0.37 | 0.77 | 19 | empty |
| 4 | 68 | 0.33 | 0.76 | 14 | empty |
| 5 | 71 | 0.28 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1248 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7PN0 · 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 A0A7G5B4V6
- Elsewhere: RCSB PDB 7PN0 · PDBe 7PN0 · UniProt A0A7G5B4V6
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