Research workbench
Crystal structure of isoform 2 of uridine phosphorylase from schistosoma mansoni in complex with citrate
Analyse Crystal structure of isoform 2 of uridine phosphorylase from schistosoma… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CYF
- Type
- protein
- Length
- 857 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uridine phosphorylase
- EC
- 2.4.2.3
- UniProt
- G4VGH9
- Pockets
- 14 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative uridine phosphorylase (EC 2.4.2.3) | protein | 290 | 36% helix, 25% strand | G4VGH9 |
| B | Putative uridine phosphorylase (EC 2.4.2.3) | protein | 288 | 36% helix, 25% strand | G4VGH9 |
| C | Putative uridine phosphorylase (EC 2.4.2.3) | protein | 279 | 34% helix, 26% strand | G4VGH9 |
Ligands and binding sites
- FLC · Citrate anion · additive · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 863 | 0.83 | 0.85 | 98 | FLC |
| 2 | 287 | 0.75 | 0.88 | 33 | empty |
| 3 | 292 | 0.74 | 0.87 | 41 | empty |
| 4 | 153 | 0.46 | 0.77 | 24 | FLC |
| 5 | 63 | 0.45 | 0.82 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2427 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 436 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 329 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5CYF · Crystal structure of isoform 2 of uridine phosphorylase from Schistosoma mansoni in… · the same entry in another collection · chain A against A, TM-score 1.00
- G4VGH9 · AlphaFold monomer V2.0 prediction for inactive uridine phosphorylase B (G4VGH9) · a predicted model of the same protein · chain C 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 G4VGH9
- Elsewhere: RCSB PDB 5CYF · PDBe 5CYF · UniProt G4VGH9
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