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X-ray structure of uridine phosphorylase from vibrio cholerae in complex with uridine and sulfate ion at 1.29 a resolution
Analyse X-ray structure of uridine phosphorylase from vibrio cholerae in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LHV
- Type
- protein
- Length
- 1,503 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
- URI, URA, MG, NA, SO4, CL
- Pockets
- 18 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, F | Uridine phosphorylase (EC 2.4.2.3) | protein | 251 | 34% helix, 29% strand | Q9K4U1 |
| D | Uridine phosphorylase (EC 2.4.2.3) | protein | 248 | 34% helix, 30% strand | Q9K4U1 |
Ligands and binding sites
- URI · Uridine · ligand · 6 copies · chains A, B, C, D, E, F
- URA · Uracil · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 7 copies · chains A, B, C, D, E, F
- NA · Sodium ion · metal · 3 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, E, D, F
- CL · Chloride ion · ion · 6 copies · chains A, F, B, C, D, E
- GOL · Glycerol · additive · 7 copies · chains A, E, F, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 228 | 0.70 | 0.86 | 37 | SO4, URI, URA |
| 2 | 489 | 0.69 | 0.79 | 51 | GOL |
| 3 | 219 | 0.68 | 0.85 | 33 | SO4, URI, URA |
| 4 | 438 | 0.68 | 0.80 | 47 | GOL |
| 5 | 338 | 0.65 | 0.80 | 41 | SO4, URI, URA |
Interfaces
12 interfaces between chains.
- A–B · 2065 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 2054 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 2001 Ų buried · 15 hydrogen bonds · protein-protein
- A–F · 1097 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 1092 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5LHV · X-ray structure of uridine phosphorylase from Vibrio cholerae in complex with uridine 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 5LHV · PDBe 5LHV · UniProt Q9K4U1
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