MolNFT v1 · #125957 · protein
X-ray structure of uridine phosphorylase from vibrio cholerae in complex with cytidine and cytosine at 1.11 a resolution
5LOK: “X-ray structure of uridine phosphorylase from vibrio cholerae in complex with cytidine and cytosine at 1.11 a…”. X-ray diffraction, 5 ligands (CYT, CTN, K), 15 pockets (best druggability 0.77). MolNFT v1 #125957 on GenesisL1: 3D…
- PDB
- 5LOK
- Type
- protein
- Length
- 1,509 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridine phosphorylase
- EC
- 2.4.2.3
- UniProt
- Q9K4U1
- Ligands
- CYT, CTN, K, CL, SO4
- Pockets
- 15 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, F | Uridine phosphorylase (EC 2.4.2.3) | protein | 251 | 33% helix, 29% strand | Q9K4U1 |
| B, C, E | Uridine phosphorylase (EC 2.4.2.3) | protein | 252 | 34% helix, 29% strand | Q9K4U1 |
Ligands and binding sites
- CYT · 6-aminopyrimidin-2(1H)-one · ligand · 7 copies · chains A, B, C, D, E, F
- CTN · 4-amino-1-beta-D-ribofuranosyl-2(1H)-pyrimidinone · ligand · 6 copies · chains A, B, C, D, E, F
- K · Potassium ion · metal · 3 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · chains A, B
- GOL · Glycerol · additive · 6 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 224 | 0.77 | 0.91 | 47 | CTN, CYT, GOL, SO4 |
| 2 | 432 | 0.72 | 0.82 | 79 | EDO |
| 3 | 238 | 0.72 | 0.87 | 38 | CTN, CYT, GOL |
| 4 | 309 | 0.70 | 0.83 | 43 | CL, CTN, CYT, GOL |
| 5 | 354 | 0.69 | 0.82 | 48 | CL, CTN, CYT, GOL |
Interfaces
12 interfaces between chains.
- C–D · 2159 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 2045 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 2006 Ų buried · 15 hydrogen bonds · protein-protein
- A–F · 1088 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 1074 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5LOK · X-ray structure of uridine phosphorylase from Vibrio cholerae in complex with cytidine… · 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 Q9K4U1
- Elsewhere: RCSB PDB 5LOK · PDBe 5LOK · UniProt Q9K4U1
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