Research workbench
Uridine phosphorylase from E. COLI, refined in the monoclinic crystal lattice
Analyse Uridine phosphorylase from E. COLI, refined in the monoclinic crystal lattice in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1K3F
- Type
- protein
- Length
- 1,518 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
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Uridine phosphorylase (EC 2.4.2.3) | protein | 253 | 26% helix, 26% strand | P12758 |
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 892 | 0.80 | 0.83 | 76 | empty |
| 2 | 338 | 0.80 | 0.90 | 48 | empty |
| 3 | 1160 | 0.78 | 0.80 | 106 | empty |
| 4 | 663 | 0.78 | 0.83 | 47 | empty |
| 5 | 990 | 0.77 | 0.79 | 66 | empty |
Interfaces
12 interfaces between chains.
- A–D · 1940 Ų buried · 16 hydrogen bonds · protein-protein
- C–E · 1871 Ų buried · 10 hydrogen bonds · protein-protein
- B–F · 1772 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 1099 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 1051 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1K3F · Uridine Phosphorylase from E. coli, Refined in the Monoclinic Crystal Lattice · the same entry in another collection · chain C against C, 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 0.93
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 1K3F · PDBe 1K3F · UniProt P12758
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