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Crystal structure of the uridine phosphorylase from salmonella typhimurium in complex with thymine and phosphate ion at 1.70A resolution
Analyse Crystal structure of the uridine phosphorylase from salmonella typhimurium in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HRD
- Type
- protein
- Length
- 1,483 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridine phosphorylase
- EC
- 2.4.2.3
- UniProt
- P0A1F6
- Ligands
- TDR, PO4
- Pockets
- 17 · best druggability 0.73
Structure
x-ray diffraction · 6 distinct chains · 33% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridine phosphorylase (EC 2.4.2.3) | protein | 251 | 33% helix, 29% strand | P0A1F6 |
| B | Uridine phosphorylase (EC 2.4.2.3) | protein | 246 | 32% helix, 30% strand | P0A1F6 |
| C | Uridine phosphorylase (EC 2.4.2.3) | protein | 245 | 32% helix, 30% strand | P0A1F6 |
| D | Uridine phosphorylase (EC 2.4.2.3) | protein | 244 | 32% helix, 30% strand | P0A1F6 |
| E | Uridine phosphorylase (EC 2.4.2.3) | protein | 252 | 35% helix, 29% strand | P0A1F6 |
| F | Uridine phosphorylase (EC 2.4.2.3) | protein | 245 | 32% helix, 29% strand | P0A1F6 |
Ligands and binding sites
- TDR · Thymine · ligand · 6 copies · chains A, B, C, D, E, F
- PO4 · Phosphate ion · ion · 8 copies · chains A, F, B, C, D, E
- GOL · Glycerol · additive · 5 copies · chains A, E, B, D, C, F
- 1PE · Pentaethylene glycol · additive · chains 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 602 | 0.73 | 0.80 | 69 | empty |
| 2 | 511 | 0.71 | 0.80 | 48 | PO4 |
| 3 | 356 | 0.69 | 0.82 | 39 | PO4, TDR |
| 4 | 257 | 0.66 | 0.83 | 46 | PO4, TDR |
| 5 | 247 | 0.65 | 0.82 | 37 | PO4, TDR |
Interfaces
12 interfaces between chains.
- B–D · 2201 Ų buried · 28 hydrogen bonds · protein-protein
- C–E · 2195 Ų buried · 29 hydrogen bonds · protein-protein
- A–F · 2159 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1027 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 1024 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2HRD · Crystal structure of the uridine phosphorylase from Salmonella typhimurium in complex… · 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 P0A1F6
- Elsewhere: RCSB PDB 2HRD · PDBe 2HRD · UniProt P0A1F6
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