MolNFT v1 · #64557 · protein
Asymetric GTP bound structure of uprtase from sulfolobus solfataricus containing prpp-MG2+ in half of the active sites and R5P and ppi in the other half
3G6W · Uracil phosphoribosyltransferase: “Asymetric GTP bound structure of uprtase from sulfolobus solfataricus containing prpp-MG2+ in half of the…”. X-ray diffraction, 5 ligands (GTP, HSX, PRP), 7 pockets (best druggability 0.81). MolNFT…
- PDB
- 3G6W
- Type
- protein
- Length
- 843 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uracil phosphoribosyltransferase
- EC
- 2.4.2.9
- UniProt
- Q980Q4
- Ligands
- GTP, HSX, PRP, POP, MG
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Uracil phosphoribosyltransferase (EC 2.4.2.9) | protein | 215 | 34% helix, 27% strand | Q980Q4 |
| B | Uracil phosphoribosyltransferase (EC 2.4.2.9) | protein | 206 | 35% helix, 30% strand | Q980Q4 |
| C | Uracil phosphoribosyltransferase (EC 2.4.2.9) | protein | 207 | 35% helix, 30% strand | Q980Q4 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains A, B, D, C
- HSX · 5-O-phosphono-alpha-D-ribofuranose · ligand · 3 copies · chains B, C, D
- PRP · 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose · ligand · 2 copies · chains A, C, B, D
- POP · Pyrophosphate 2- · ligand · 2 copies · chains B, D, A, C
- MG · Magnesium ion · metal · 4 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1136 | 0.81 | 0.82 | 102 | GTP, MG |
| 2 | 327 | 0.73 | 0.85 | 33 | PRP, MG |
| 3 | 304 | 0.72 | 0.85 | 32 | PRP, HSX, MG |
| 4 | 330 | 0.70 | 0.83 | 29 | HSX, POP |
| 5 | 330 | 0.68 | 0.82 | 32 | HSX, POP |
Interfaces
4 interfaces between chains.
- C–D · 1699 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1678 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 1051 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 1046 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3G6W · Asymetric GTP bound structure of UPRTase from Sulfolobus solfataricus containing… · the same entry in another collection · chain A against A, TM-score 1.00
- Q980Q4 · AlphaFold monomer V2.0 prediction for uracil phosphoribosyltransferase (Q980Q4) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q980Q4
- Elsewhere: RCSB PDB 3G6W · PDBe 3G6W · UniProt Q980Q4
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