MolNFT v1 · #75357 · protein
Crystal structure of uridine phosphorylase complexed with uracil from vibrio cholerae O1 biovar el tor
3PNS: “Crystal structure of uridine phosphorylase complexed with uracil from vibrio cholerae O1 biovar el tor”. X-ray diffraction, 3 ligands (URA, CL, SO4), 20 pockets (best druggability 0.74). MolNFT v1 #75357 on GenesisL1: 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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