MolNFT v1 · #117684 · protein
X-ray structure uridine phosphorylase from vibrio cholerae in complex with cytidine and cytosine at 1.63A.
5EFO: “X-ray structure uridine phosphorylase from vibrio cholerae in complex with cytidine and cytosine at 1.63A.”. X-ray diffraction, 3 ligands (CYT, CTN, NA), 16 pockets (best druggability 0.74). MolNFT v1 #117684 on GenesisL1: 3D…
- PDB
- 5EFO
- Type
- protein
- Length
- 1,505 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, NA
- Pockets
- 16 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridine phosphorylase (EC 2.4.2.3) | protein | 248 | 33% helix, 29% strand | Q9K4U1 |
| B | Uridine phosphorylase (EC 2.4.2.3) | protein | 253 | 34% helix, 28% strand | Q9K4U1 |
| C, D, E, F | Uridine phosphorylase (EC 2.4.2.3) | protein | 251 | 34% helix, 28% strand | Q9K4U1 |
Ligands and binding sites
- CYT · 6-aminopyrimidin-2(1H)-one · ligand · 6 copies · chains A, B, C, D, E, F
- CTN · 4-amino-1-beta-D-ribofuranosyl-2(1H)-pyrimidinone · ligand · 2 copies · chains E, F
- NA · Sodium ion · metal · 3 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 3 copies · chains D, E, F
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 191 | 0.74 | 0.90 | 39 | GOL, CTN |
| 2 | 426 | 0.73 | 0.83 | 47 | GOL, CYT |
| 3 | 509 | 0.73 | 0.81 | 74 | CYT, EDO |
| 4 | 418 | 0.72 | 0.82 | 41 | CYT, TRS |
| 5 | 508 | 0.70 | 0.80 | 57 | GOL, CYT |
Interfaces
12 interfaces between chains.
- E–F · 2095 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1941 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1938 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 1075 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 1071 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5EFO · X-ray structure uridine phosphorylase from Vibrio cholerae in complex with cytidine and… · 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 5EFO · PDBe 5EFO · UniProt Q9K4U1
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