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The (P)PPGPP-bound crystal structure of hprt (hypoxanthine phosphoribosyltransferase)
Analyse The (P)PPGPP-bound crystal structure of hprt (hypoxanthine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D9S
- Type
- protein
- Length
- 360 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypoxanthine phosphoribosyltransferase
- EC
- 2.4.2.8
- UniProt
- A0A1S0QLD4
- Ligands
- G4P, MG
- Pockets
- 2 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hypoxanthine phosphoribosyltransferase (EC 2.4.2.8) | protein | 180 | 29% helix, 32% strand | A0A1S0QLD4 |
Ligands and binding sites
- G4P · Guanosine-5',3'-tetraphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 353 | 0.60 | 0.76 | 29 | G4P, MG |
| 2 | 366 | 0.58 | 0.75 | 29 | G4P |
Interfaces
1 interface between chains.
- A–B · 950 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 6D9S · The (p)ppGpp-bound crystal structure of HPRT (hypoxanthine phosphoribosyltransferase) · 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 A0A1S0QLD4
- Elsewhere: RCSB PDB 6D9S · PDBe 6D9S · UniProt A0A1S0QLD4
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