Research workbench
Structure of E. COLI uridine phosphorylase complexed to 5-(M- (BENZYLOXY)BENZYL)BARBITURIC acid (bbba)
Analyse Structure of E. COLI uridine phosphorylase complexed to 5-(M… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1U1G
- Type
- protein
- Length
- 1,493 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridine phosphorylase
- EC
- 2.4.2.3
- UniProt
- P12758
- Ligands
- BBB, K
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridine phosphorylase (EC 2.4.2.3) | protein | 245 | 35% helix, 30% strand | P12758 |
| B | Uridine phosphorylase (EC 2.4.2.3) | protein | 251 | 34% helix, 29% strand | P12758 |
| C, D, F | Uridine phosphorylase (EC 2.4.2.3) | protein | 250 | 34% helix, 28% strand | P12758 |
| E | Uridine phosphorylase (EC 2.4.2.3) | protein | 247 | 35% helix, 30% strand | P12758 |
Ligands and binding sites
- BBB · 1-((2-hydroxyethoxy)methyl)-5-(3-(benzyloxy)benzyl)-6-hydroxypyrimidine-2,4(1H,3H)-dione · ligand · 6 copies · chains A, B, C, D, E, F
- K · Potassium ion · metal · 3 copies · chains A, B, C, D, E, 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 436 | 0.74 | 0.83 | 50 | BBB |
| 2 | 483 | 0.73 | 0.82 | 43 | BBB |
| 3 | 411 | 0.73 | 0.83 | 64 | empty |
| 4 | 449 | 0.72 | 0.82 | 44 | BBB |
| 5 | 465 | 0.72 | 0.82 | 45 | BBB |
Interfaces
12 interfaces between chains.
- E–F · 2101 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 2088 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 2087 Ų buried · 24 hydrogen bonds · protein-protein
- B–F · 1063 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 1058 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1U1G · Structure of E. coli uridine phosphorylase complexed to 5-(m-(benzyloxy)benzyl)barbituric… · the same entry in another collection · chain F against F, TM-score 1.00
- P12758 · AlphaFold monomer V2.0 prediction for uridine phosphorylase (P12758) · a predicted model of the same protein · 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 P12758
- Elsewhere: RCSB PDB 1U1G · PDBe 1U1G · UniProt P12758
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.