MolNFT v1 · #27779 · protein
Sulfolobus solfataricus uracil phosphoribosyltransferase with uridine 5'-monophosphate (ump) bound to half of the subunits
1XTV · Probable uracil phosphoribosyltransferase: “Sulfolobus solfataricus uracil phosphoribosyltransferase with uridine 5'-monophosphate (ump) bound to half of…”. X-ray diffraction, 1 ligand (U5P), 20 pockets (best druggability 0.85).…
- PDB
- 1XTV
- Type
- protein
- Length
- 1,720 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable uracil phosphoribosyltransferase
- EC
- 2.4.2.9
- UniProt
- Q980Q4
- Ligands
- U5P
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Probable uracil phosphoribosyltransferase (EC 2.4.2.9) | protein | 215 | 35% helix, 30% strand | Q980Q4 |
Ligands and binding sites
- U5P · Uridine-5'-monophosphate · ligand · 4 copies · chains A, C, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1015 | 0.85 | 0.86 | 90 | empty |
| 2 | 1122 | 0.85 | 0.86 | 108 | empty |
| 3 | 128 | 0.77 | 0.95 | 24 | U5P |
| 4 | 293 | 0.77 | 0.89 | 35 | U5P |
| 5 | 124 | 0.76 | 0.95 | 24 | U5P |
Interfaces
11 interfaces between chains.
- C–D · 1849 Ų buried · 24 hydrogen bonds · protein-protein
- G–H · 1840 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1827 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 1824 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1122 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1XTV · Sulfolobus solfataricus uracil phosphoribosyltransferase with uridine 5'-monophosphate… · the same entry in another collection · chain H against H, 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 0.98
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 1XTV · PDBe 1XTV · UniProt Q980Q4
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