Research workbench
Crystal structure of the uridine phosphorylase from salmonella typhimurium in complex with uridine-5P-monophosphate and sulfate ion at 2.35A resolution
Analyse Crystal structure of the uridine phosphorylase from salmonella typhimurium in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Y1Q
- Type
- protein
- Length
- 1,456 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridine phosphorylase
- EC
- 2.4.2.3
- UniProt
- P0A1F6
- Ligands
- U, SO4
- Pockets
- 15 · best druggability 0.71
Structure
x-ray diffraction · 6 distinct chains · 32% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridine phosphorylase (EC 2.4.2.3) | protein | 250 | 32% helix, 28% strand | P0A1F6 |
| B | Uridine phosphorylase (EC 2.4.2.3) | protein | 239 | 32% helix, 27% strand | P0A1F6 |
| C | Uridine phosphorylase (EC 2.4.2.3) | protein | 240 | 33% helix, 30% strand | P0A1F6 |
| D | Uridine phosphorylase (EC 2.4.2.3) | protein | 245 | 34% helix, 29% strand | P0A1F6 |
| E | Uridine phosphorylase (EC 2.4.2.3) | protein | 238 | 31% helix, 31% strand | P0A1F6 |
| F | Uridine phosphorylase (EC 2.4.2.3) | protein | 244 | 32% helix, 30% strand | P0A1F6 |
Ligands and binding sites
- U · Uridine-5'-monophosphate · ligand · chains C, F
- SO4 · Sulfate ion · ion · 4 copies · chains A, D, E, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 459 | 0.71 | 0.81 | 51 | SO4 |
| 2 | 435 | 0.71 | 0.81 | 37 | empty |
| 3 | 393 | 0.69 | 0.81 | 42 | empty |
| 4 | 364 | 0.68 | 0.81 | 34 | empty |
| 5 | 253 | 0.68 | 0.84 | 35 | SO4 |
Interfaces
12 interfaces between chains.
- C–F · 2141 Ų buried · 26 hydrogen bonds · protein-protein
- A–E · 2090 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 1971 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 1028 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 1021 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1Y1Q · Crystal Structure of the Uridine Phosphorylase from Salmonella Typhimurium in Complex… · the same entry in another collection · chain A against A, 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 P0A1F6
- Elsewhere: RCSB PDB 1Y1Q · PDBe 1Y1Q · UniProt P0A1F6
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