Research workbench
Trapping of an oxocarbenium ion intermediate in up crystals
Analyse Trapping of an oxocarbenium ion intermediate in up crystals in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KUK
- Type
- protein
- Length
- 583 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridine phosphorylase
- EC
- 2.4.2.3
- UniProt
- A5PJH9
- Ligands
- DUR, SO4
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridine phosphorylase (EC 2.4.2.3) | protein | 290 | 37% helix, 27% strand | A5PJH9 |
| B | Uridine phosphorylase (EC 2.4.2.3) | protein | 293 | 35% helix, 26% strand | A5PJH9 |
Ligands and binding sites
- DUR · 2'-deoxyuridine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 128 | 0.78 | 0.96 | 34 | SO4, DUR |
| 2 | 405 | 0.77 | 0.86 | 48 | empty |
| 3 | 86 | 0.75 | 0.98 | 26 | SO4, DUR |
| 4 | 205 | 0.61 | 0.82 | 33 | empty |
| 5 | 211 | 0.54 | 0.78 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 2930 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 3KUK · Trapping of an oxocarbenium ion intermediate in UP crystals · 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 A5PJH9
- Elsewhere: RCSB PDB 3KUK · PDBe 3KUK · UniProt A5PJH9
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