Research workbench
Hypoxanthine-guanine-xanthine phosphoribosyltransferase (hgxprt) from sulfolobus solfataricus with sulfate bound in the 5-phosphoribosyl 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
- 5BQO
- Type
- protein
- Length
- 1,037 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purine phosphoribosyltransferase (gpt-2)
- EC
- 2.4.2.8
- UniProt
- Q97W22
- Ligands
- SO4
- Pockets
- 16 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Purine phosphoribosyltransferase (gpt-2) (EC 2.4.2.8) | protein | 169 | 35% helix, 28% strand | Q97W22 |
| B, D | Purine phosphoribosyltransferase (gpt-2) (EC 2.4.2.8) | protein | 177 | 33% helix, 27% strand | Q97W22 |
| C | Purine phosphoribosyltransferase (gpt-2) (EC 2.4.2.8) | protein | 168 | 36% helix, 27% strand | Q97W22 |
| E | Purine phosphoribosyltransferase (gpt-2) (EC 2.4.2.8) | protein | 177 | 33% helix, 26% strand | Q97W22 |
| F | Purine phosphoribosyltransferase (gpt-2) (EC 2.4.2.8) | protein | 169 | 34% helix, 27% strand | Q97W22 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 903 | 0.78 | 0.81 | 62 | SO4 |
| 2 | 521 | 0.74 | 0.82 | 44 | SO4 |
| 3 | 595 | 0.74 | 0.81 | 42 | SO4 |
| 4 | 151 | 0.72 | 0.91 | 33 | empty |
| 5 | 441 | 0.67 | 0.79 | 40 | SO4 |
Interfaces
8 interfaces between chains.
- C–D · 2333 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 2262 Ų buried · 32 hydrogen bonds · protein-protein
- E–F · 2237 Ų buried · 31 hydrogen bonds · protein-protein
- D–F · 739 Ų buried · 7 hydrogen bonds · protein-protein
- C–E · 724 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5BQO · Hypoxanthine-guanine-xanthine phosphoribosyltransferase (HGXPRT) from Sulfolobus… · the same entry in another collection · chain E against E, 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 5BQO · PDBe 5BQO · UniProt Q97W22
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