MolNFT v1 · #3899 · protein
Ternary complex structure of human hgprtase, prpp, MG2+, and the inhibitor hpp reveals the involvement of the flexible loop in substrate binding
1D6N · Protein (hypoxanthine-guanine phosphoribosyltransferase): “Ternary complex structure of human hgprtase, prpp, MG2+, and the inhibitor hpp reveals the involvement of the…”. X-ray diffraction, 3 ligands (PPO, PRP, MG), 6 pockets (best…
- PDB
- 1D6N
- Type
- protein
- Length
- 428 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (hypoxanthine-guanine phosphoribosyltransferase)
- EC
- 2.4.2.8
- UniProt
- P00492
- Ligands
- PPO, PRP, MG
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein (hypoxanthine-guanine phosphoribosyltransferase) (EC 2.4.2.8) | protein | 214 | 23% helix, 17% strand | P00492 |
Ligands and binding sites
- PPO · 3H-pyrazolo[4,3-d]pyrimidin-7-ol · ligand · 2 copies · chains A, B
- 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 | 462 | 0.78 | 0.86 | 58 | MG, PPO, PRP |
| 2 | 265 | 0.75 | 0.89 | 37 | MG, PPO, PRP |
| 3 | 114 | 0.50 | 0.80 | 23 | empty |
| 4 | 167 | 0.49 | 0.77 | 21 | empty |
| 5 | 123 | 0.39 | 0.74 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1367 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 1D6N · Ternary complex structure of human hgprtase, prpp, MG2+, and the inhibitor hpp reveals… · the same entry in another collection · chain A against A, TM-score 1.00
- P00492 · AlphaFold monomer V2.0 prediction for hypoxanthine-guanine phosphoribosyltransferase… · a predicted model of the same protein · chain A against A, TM-score 0.93
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 P00492
- Elsewhere: RCSB PDB 1D6N · PDBe 1D6N · UniProt P00492
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