Research workbench
Crystal structure of uridine phosphorylase complexed with uracil from vibrio cholerae O1 biovar el tor
Analyse Crystal structure of uridine phosphorylase complexed with uracil from vibrio… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PNS
- Type
- protein
- Length
- 2,968 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridine phosphorylase
- UniProt
- Q9KT71
- Ligands
- URA, CL, SO4
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 8 distinct chains · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F, G, I | Uridine phosphorylase | protein | 250 | 34% helix, 28% strand | Q9KT71 |
| B | Uridine phosphorylase | protein | 244 | 35% helix, 29% strand | Q9KT71 |
| C | Uridine phosphorylase | protein | 248 | 35% helix, 29% strand | Q9KT71 |
| D | Uridine phosphorylase | protein | 245 | 34% helix, 29% strand | Q9KT71 |
| E, L | Uridine phosphorylase | protein | 245 | 34% helix, 29% strand | Q9KT71 |
| H | Uridine phosphorylase | protein | 249 | 35% helix, 29% strand | Q9KT71 |
| J | Uridine phosphorylase | protein | 241 | 32% helix, 29% strand | Q9KT71 |
| K | Uridine phosphorylase | protein | 251 | 33% helix, 29% strand | Q9KT71 |
Ligands and binding sites
- URA · Uracil · ligand · 11 copies · chains B, C, D, E, F, G, H, I, J, K, L
- CL · Chloride ion · ion · 4 copies · chains C, E, F, I
- SO4 · Sulfate ion · ion · 3 copies · chains C, F, J, G, D, E, I
- GOL · Glycerol · additive · 24 copies · chains A, B, C, D, I, J, E, F, G, H, K, L
- FMT · Formic acid · additive · 2 copies · chains E, F, H
- ACY · Acetic acid · additive · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 673 | 0.74 | 0.80 | 66 | GOL, URA, FMT |
| 2 | 409 | 0.73 | 0.84 | 50 | GOL, URA |
| 3 | 487 | 0.73 | 0.82 | 47 | GOL, URA |
| 4 | 476 | 0.73 | 0.82 | 47 | GOL, URA |
| 5 | 560 | 0.72 | 0.80 | 50 | GOL |
Interfaces
22 interfaces between chains.
- G–H · 2003 Ų buried · 18 hydrogen bonds · protein-protein
- I–J · 1975 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1971 Ų buried · 20 hydrogen bonds · protein-protein
- K–L · 1943 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1916 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 120 modified (engineered).
Compared structures
- 3PNS · Crystal Structure of Uridine Phosphorylase Complexed with Uracil from Vibrio cholerae O1… · 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 Q9KT71
- Elsewhere: RCSB PDB 3PNS · PDBe 3PNS · UniProt Q9KT71
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