MolNFT v1 · #19430 · protein
Toxoplasma gondii hypoxanthine-guanine phosphoribosyltransferase with xmp, pyrophosphate and two MG2+ ions
1QK5: “Toxoplasma gondii hypoxanthine-guanine phosphoribosyltransferase with xmp, pyrophosphate and two MG2+ ions”. X-ray diffraction, 3 ligands (XMP, POP, MG), 6 pockets (best druggability 0.73). MolNFT v1 #19430 on GenesisL1: 3D…
- PDB
- 1QK5
- Type
- protein
- Length
- 432 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypoxanthine-guanine phosphoribosyltransferase
- EC
- 2.4.2.8
- UniProt
- Q26997
- Ligands
- XMP, POP, MG
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 215 | 30% helix, 28% strand | Q26997 |
| B | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 217 | 31% helix, 28% strand | Q26997 |
Ligands and binding sites
- XMP · Xanthosine-5'-monophosphate · ligand · 2 copies · chains A, B
- POP · Pyrophosphate 2- · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 482 | 0.73 | 0.82 | 48 | empty |
| 2 | 58 | 0.68 | 0.96 | 20 | empty |
| 3 | 295 | 0.61 | 0.79 | 33 | XMP, POP, MG |
| 4 | 309 | 0.61 | 0.78 | 28 | XMP, POP, MG |
| 5 | 50 | 0.34 | 0.79 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1505 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 1QK5 · Toxoplasma gondii hypoxanthine-guanine phosphoribosyltransferase with xmp, pyrophosphate… · the same entry in another collection · chain A against A, TM-score 1.00
- Q26997 · AlphaFold monomer V2.0 prediction for hypoxanthine-guanine-xanthine… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q26997
- Elsewhere: RCSB PDB 1QK5 · PDBe 1QK5 · UniProt Q26997
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