MolNFT v1 · #106141 · protein
Crystal structure of a hypoxanthine phosphoribosyltransferase (target id nysgrc-029686) from staphylococcus aureus (tetragonal space group)
4RQB: “Crystal structure of a hypoxanthine phosphoribosyltransferase (target id nysgrc-029686) from staphylococcus…”. X-ray diffraction, 3 ligands (UNL, SO4, CL), 3 pockets (best druggability 0.65). MolNFT v1 #106141 on GenesisL1: 3D…
- PDB
- 4RQB
- Type
- protein
- Length
- 362 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypoxanthine phosphoribosyltransferase
- EC
- 2.4.2.8
- UniProt
- A8YZK8
- Ligands
- UNL, SO4, CL
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypoxanthine phosphoribosyltransferase (EC 2.4.2.8) | protein | 184 | 28% helix, 37% strand | A8YZK8 |
| B | Hypoxanthine phosphoribosyltransferase (EC 2.4.2.8) | protein | 178 | 27% helix, 38% strand | A8YZK8 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- CL · Chloride ion · ion · chains B
- GOL · Glycerol · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 473 | 0.65 | 0.77 | 35 | SO4, UNL |
| 2 | 440 | 0.64 | 0.78 | 40 | SO4, UNL |
| 3 | 57 | 0.32 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1607 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 4RQB · Crystal Structure of a Hypoxanthine Phosphoribosyltransferase (target ID NYSGRC-029686)… · 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 A8YZK8
- Elsewhere: RCSB PDB 4RQB · PDBe 4RQB · UniProt A8YZK8
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