Research workbench
X-ray structure of uridine phosphorylease from vibrio cholerae complexed with thymidine at 2.12 a resolution
Analyse X-ray structure of uridine phosphorylease from vibrio cholerae complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4G8J
- Type
- protein
- Length
- 1,496 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
- THM, NA, MG, CL
- Pockets
- 14 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridine phosphorylase (EC 2.4.2.3) | protein | 245 | 32% helix, 29% strand | Q9K4U1 |
| B | Uridine phosphorylase (EC 2.4.2.3) | protein | 252 | 34% helix, 29% strand | Q9K4U1 |
| C, D, E | Uridine phosphorylase (EC 2.4.2.3) | protein | 251 | 34% helix, 29% strand | Q9K4U1 |
| F | Uridine phosphorylase (EC 2.4.2.3) | protein | 246 | 32% helix, 29% strand | Q9K4U1 |
Ligands and binding sites
- THM · Thymidine · ligand · 6 copies · chains A, B, C, D, E, F
- NA · Sodium ion · metal · 3 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 2 copies · chains A, F
- CL · Chloride ion · ion · 9 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 4 copies · chains C, D, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1095 | 0.79 | 0.81 | 128 | EDO |
| 2 | 318 | 0.71 | 0.84 | 36 | THM, EDO, CL |
| 3 | 302 | 0.70 | 0.84 | 42 | THM, CL |
| 4 | 329 | 0.70 | 0.83 | 38 | THM, CL |
| 5 | 203 | 0.70 | 0.87 | 37 | THM, CL |
Interfaces
12 interfaces between chains.
- C–D · 2039 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 2038 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 2016 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 1082 Ų buried · 6 hydrogen bonds · protein-protein
- A–F · 1079 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4G8J · X-ray Structure of Uridine Phosphorylease from Vibrio cholerae Complexed with Thymidine… · 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 4G8J · PDBe 4G8J · UniProt Q9K4U1
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