MolNFT v1 · #111805 · protein
Hypoxanthine-guanine-xanthine phosphoribosyltransferase (hgxprt) from sulfolobus solfataricus in complex with alpha- phosphoribosylpyrophosphoric acid (prpp) and magnesium
4Z1O: “Hypoxanthine-guanine-xanthine phosphoribosyltransferase (hgxprt) from sulfolobus solfataricus in complex with…”. X-ray diffraction, 2 ligands (PRP, MG), 6 pockets (best druggability 0.75). MolNFT v1 #111805 on GenesisL1: 3D…
- PDB
- 4Z1O
- Type
- protein
- Length
- 347 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoribosyltransferase
- EC
- 2.4.2.8
- UniProt
- D0KMY9
- Ligands
- PRP, MG
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoribosyltransferase (EC 2.4.2.8) | protein | 171 | 35% helix, 25% strand | D0KMY9 |
| B | Phosphoribosyltransferase (EC 2.4.2.8) | protein | 176 | 34% helix, 27% strand | D0KMY9 |
Ligands and binding sites
- PRP · 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 615 | 0.75 | 0.81 | 47 | PRP, MG |
| 2 | 514 | 0.73 | 0.82 | 42 | PRP, MG |
| 3 | 76 | 0.35 | 0.76 | 17 | empty |
| 4 | 63 | 0.35 | 0.77 | 15 | empty |
| 5 | 60 | 0.30 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 2295 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 4Z1O · Hypoxanthine-guanine-xanthine phosphoribosyltransferase (HGXPRT) from Sulfolobus… · 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 D0KMY9
- Elsewhere: RCSB PDB 4Z1O · PDBe 4Z1O · UniProt D0KMY9
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