Research workbench
The substrate-bound crystal structure of hprt (hypoxanthine phosphoribosyltransferase)
Analyse The substrate-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
- 6D9R
- Type
- protein
- Length
- 346 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
- 9DG, PRP, MG
- Pockets
- 3 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hypoxanthine phosphoribosyltransferase (EC 2.4.2.8) | protein | 173 | 29% helix, 33% strand | A0A1S0QLD4 |
Ligands and binding sites
- 9DG · 9-deazaguanine · 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 · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, B
- ACT · Acetate ion · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 316 | 0.58 | 0.77 | 35 | 9DG, PRP, MG |
| 2 | 290 | 0.58 | 0.77 | 32 | 9DG, PRP, MG |
| 3 | 121 | 0.51 | 0.81 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1719 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 6D9R · The substrate-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 6D9R · PDBe 6D9R · UniProt A0A1S0QLD4
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