Research workbench
Crystal structure of uracil phosphoribosyltransferase (TM0721) from thermotoga maritima at 2.30 a resolution
Analyse Crystal structure of uracil phosphoribosyltransferase (TM0721) from thermotoga… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1O5O
- Type
- protein
- Length
- 839 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uracil phosphoribosyltransferase
- EC
- 2.4.2.9
- UniProt
- Q9WZI0
- Ligands
- U5P, SO4
- Pockets
- 13 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Uracil phosphoribosyltransferase (EC 2.4.2.9) | protein | 210 | 33% helix, 29% strand | Q9WZI0 |
| B | Uracil phosphoribosyltransferase (EC 2.4.2.9) | protein | 209 | 33% helix, 29% strand | Q9WZI0 |
Ligands and binding sites
- U5P · Uridine-5'-monophosphate · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 9 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1167 | 0.87 | 0.87 | 65 | empty |
| 2 | 269 | 0.76 | 0.89 | 35 | SO4, U5P |
| 3 | 273 | 0.76 | 0.89 | 30 | SO4, U5P |
| 4 | 392 | 0.74 | 0.84 | 33 | SO4, U5P |
| 5 | 376 | 0.73 | 0.84 | 32 | SO4, U5P |
Interfaces
6 interfaces between chains.
- C–D · 2137 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 2091 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 1224 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1200 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 88 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1O5O · Crystal structure of Uracil phosphoribosyltransferase (TM0721) from Thermotoga maritima… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9WZI0 · AlphaFold monomer V2.0 prediction for uracil phosphoribosyltransferase (Q9WZI0) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q9WZI0
- Elsewhere: RCSB PDB 1O5O · PDBe 1O5O · UniProt Q9WZI0
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