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X-ray structure uridine phosphorylase from vibrio cholerae in complex with thymine at 1.25 a resolution
Analyse X-ray structure 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
- 4OGL
- Type
- protein
- Length
- 1,502 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridine phosphorylase
- EC
- 2.4.2.3
- UniProt
- Q9KT71
- Ligands
- TDR, NA
- Pockets
- 17 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridine phosphorylase (EC 2.4.2.3) | protein | 247 | 32% helix, 30% strand | Q9KT71 |
| B, C, D, E | Uridine phosphorylase (EC 2.4.2.3) | protein | 251 | 34% helix, 29% strand | Q9KT71 |
| F | Uridine phosphorylase (EC 2.4.2.3) | protein | 251 | 32% helix, 29% strand | Q9KT71 |
Ligands and binding sites
- TDR · Thymine · ligand · 6 copies · chains A, B, C, D, E, F
- NA · Sodium ion · metal · 3 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, F, C, D, E
- GOL · Glycerol · additive · 6 copies · chains A, B, C, D, E, F
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 326 | 0.75 | 0.87 | 57 | TDR, GOL |
| 2 | 393 | 0.75 | 0.85 | 44 | TDR, GOL |
| 3 | 402 | 0.74 | 0.84 | 47 | TDR, GOL |
| 4 | 271 | 0.73 | 0.87 | 38 | TDR, GOL, EDO |
| 5 | 344 | 0.70 | 0.83 | 46 | TDR, GOL |
Interfaces
12 interfaces between chains.
- A–B · 2035 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 2029 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1997 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 1094 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 1085 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4OGL · X-ray structure uridine phosphorylase from Vibrio cholerae in complex with thymine at… · 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 Q9KT71
- Elsewhere: RCSB PDB 4OGL · PDBe 4OGL · UniProt Q9KT71
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