MolNFT v1 · #151210 · protein
Crystal structure of human aprt wild type in complex with hypoxanthine, prpp and MG2+
6HGQ · Adenine phosphoribosyltransferase: “Crystal structure of human aprt wild type in complex with hypoxanthine, prpp and MG2+”. X-ray diffraction, 3 ligands (PRP, HPA, MG), 5 pockets (best druggability 0.79). MolNFT v1 #151210 on…
- PDB
- 6HGQ
- Type
- protein
- Length
- 709 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenine phosphoribosyltransferase
- EC
- 2.4.2.7
- UniProt
- P07741
- Ligands
- PRP, HPA, MG
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Adenine phosphoribosyltransferase (EC 2.4.2.7) | protein | 179 | 35% helix, 35% strand | P07741 |
| D | Adenine phosphoribosyltransferase (EC 2.4.2.7) | protein | 177 | 34% helix, 36% strand | P07741 |
| B | Adenine phosphoribosyltransferase (EC 2.4.2.7) | protein | 174 | 35% helix, 36% strand | P07741 |
Ligands and binding sites
- PRP · 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose · ligand · 4 copies · chains A, B, C, D
- HPA · Hypoxanthine · ligand · 4 copies · chains A, C, D, B
- MG · Magnesium ion · metal · 4 copies · chains A, C, D, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 414 | 0.79 | 0.87 | 66 | MG, PRP, HPA |
| 2 | 379 | 0.78 | 0.88 | 65 | MG, PRP, HPA |
| 3 | 694 | 0.72 | 0.79 | 57 | empty |
| 4 | 99 | 0.41 | 0.77 | 16 | empty |
| 5 | 52 | 0.28 | 0.74 | 12 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1597 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1574 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 504 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 23 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6HGQ · Crystal Structure of Human APRT wild type in complex with Hypoxanthine, PRPP and Mg2+ · the same entry in another collection · chain B against B, TM-score 1.00
- P07741 · AlphaFold monomer V2.0 prediction for adenine phosphoribosyltransferase (P07741) · a predicted model of the same protein · chain B 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 P07741
- Elsewhere: RCSB PDB 6HGQ · PDBe 6HGQ · UniProt P07741
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