MolNFT v1 · #39350 · protein
Crystal structure of the uridine phosphorylase from salmonella typhimurium in complex with thymine and phosphate ion at 1.70A resolution
2HRD: “Crystal structure of the uridine phosphorylase from salmonella typhimurium in complex with thymine and…”. X-ray diffraction, 2 ligands (TDR, PO4), 17 pockets (best druggability 0.73). MolNFT v1 #39350 on GenesisL1: 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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