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Hypoxanthine-guanine-xanthine phosphoribosyltransferase (hgxprt) from sulfolobus solfataricus with xanthosine and phosphate bound in the nucleotide binding site and with sulfate bound in the pyrophosphate binding site
Analyse Hypoxanthine-guanine-xanthine phosphoribosyltransferase (hgxprt) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BQP
- Type
- protein
- Length
- 682 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purine phosphoribosyltransferase (gpt-2)
- EC
- 2.4.2.-
- UniProt
- Q97W22
- Ligands
- 4UO, SO4, PO4
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Purine phosphoribosyltransferase (gpt-2) (EC 2.4.2.-) | protein | 169 | 36% helix, 27% strand | Q97W22 |
| B | Purine phosphoribosyltransferase (gpt-2) (EC 2.4.2.-) | protein | 167 | 35% helix, 28% strand | Q97W22 |
| C | Purine phosphoribosyltransferase (gpt-2) (EC 2.4.2.-) | protein | 170 | 35% helix, 27% strand | Q97W22 |
| D | Purine phosphoribosyltransferase (gpt-2) (EC 2.4.2.-) | protein | 176 | 33% helix, 28% strand | Q97W22 |
Ligands and binding sites
- 4UO · 2,3-dihydroxanthosine · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B, D
- GOL · Glycerol · additive · 2 copies · chains B, C
- PGE · Triethylene glycol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 650 | 0.72 | 0.79 | 43 | 4UO, PO4, SO4 |
| 2 | 278 | 0.59 | 0.78 | 28 | 4UO, PO4, SO4, PG4 |
| 3 | 410 | 0.58 | 0.75 | 51 | empty |
| 4 | 250 | 0.57 | 0.78 | 26 | 4UO, PO4, SO4 |
| 5 | 240 | 0.53 | 0.76 | 25 | 4UO, PO4, SO4 |
Interfaces
4 interfaces between chains.
- C–D · 745 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 695 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 501 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 341 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5BQP · Hypoxanthine-guanine-xanthine phosphoribosyltransferase (HGXPRT) from Sulfolobus… · the same entry in another collection · chain B against B, 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 Q97W22
- Elsewhere: RCSB PDB 5BQP · PDBe 5BQP · UniProt Q97W22
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