MolNFT v1 · #21019 · protein
E. COLI uridine phosphorylase: 5-fluorouracil ribose-1-phosphate complex
1RXC: “E. COLI uridine phosphorylase: 5-fluorouracil ribose-1-phosphate complex”. X-ray diffraction, 5 ligands (R1P, URF, 5UD), 20 pockets (best druggability 0.80). MolNFT v1 #21019 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1RXC
- Type
- protein
- Length
- 2,970 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridine phosphorylase
- EC
- 2.4.2.3
- UniProt
- P12758
- Ligands
- R1P, URF, 5UD, K, PO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 33% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridine phosphorylase (EC 2.4.2.3) | protein | 246 | 33% helix, 29% strand | P12758 |
| B, D, E, F, I, J, L | Uridine phosphorylase (EC 2.4.2.3) | protein | 250 | 32% helix, 28% strand | P12758 |
| C | Uridine phosphorylase (EC 2.4.2.3) | protein | 246 | 33% helix, 30% strand | P12758 |
| G | Uridine phosphorylase (EC 2.4.2.3) | protein | 245 | 34% helix, 27% strand | P12758 |
| H | Uridine phosphorylase (EC 2.4.2.3) | protein | 240 | 33% helix, 30% strand | P12758 |
| K | Uridine phosphorylase (EC 2.4.2.3) | protein | 243 | 33% helix, 30% strand | P12758 |
Ligands and binding sites
- R1P · 1-O-phosphono-alpha-D-ribofuranose · ligand · 8 copies · chains A, B, C, D, E, F, I, J, K, L
- URF · 5-fluorouracil · ligand · 8 copies · chains B, C, D, E, F, I, K, L
- 5UD · 5-fluorouridine · ligand · chains I, J
- K · Potassium ion · metal · 5 copies · chains A, B, C, D, E, F, I, J, K, L
- PO4 · Phosphate ion · ion · chains I, J
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 | 1125 | 0.80 | 0.81 | 107 | empty |
| 2 | 1062 | 0.80 | 0.81 | 113 | empty |
| 3 | 221 | 0.70 | 0.86 | 36 | R1P, URF |
| 4 | 379 | 0.70 | 0.82 | 38 | empty |
| 5 | 319 | 0.70 | 0.83 | 38 | empty |
Interfaces
26 interfaces between chains.
- K–L · 2100 Ų buried · 23 hydrogen bonds · protein-protein
- I–J · 2098 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 2097 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 2095 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 2030 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 1RXC · E. COLI uridine phosphorylase: 5-fluorouracil ribose-1-phosphate complex · the same entry in another collection · chain L against L, 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 P12758
- Elsewhere: RCSB PDB 1RXC · PDBe 1RXC · UniProt P12758
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