MolNFT v1 · #39532 · protein
Crystal structure of the uridine phosphorylase from salmonella typhimurium in complex with uridine and phosphate ion at 2.91A resolution
2HWU: “Crystal structure of the uridine phosphorylase from salmonella typhimurium in complex with uridine and…”. X-ray diffraction, 2 ligands (URI, PO4), 16 pockets (best druggability 0.71). MolNFT v1 #39532 on GenesisL1: 3D structure…
- PDB
- 2HWU
- Type
- protein
- Length
- 1,466 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
- URI, PO4
- Pockets
- 16 · best druggability 0.71
Structure
x-ray diffraction · 6 distinct chains · 31% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridine phosphorylase (EC 2.4.2.3) | protein | 253 | 32% helix, 28% strand | P0A1F6 |
| B | Uridine phosphorylase (EC 2.4.2.3) | protein | 242 | 31% helix, 29% strand | P0A1F6 |
| C | Uridine phosphorylase (EC 2.4.2.3) | protein | 243 | 33% helix, 29% 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 | 242 | 32% helix, 30% strand | P0A1F6 |
| F | Uridine phosphorylase (EC 2.4.2.3) | protein | 242 | 29% helix, 29% strand | P0A1F6 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 505 | 0.71 | 0.80 | 69 | empty |
| 2 | 413 | 0.70 | 0.81 | 42 | empty |
| 3 | 350 | 0.67 | 0.81 | 47 | PO4, URI |
| 4 | 327 | 0.66 | 0.81 | 48 | URI |
| 5 | 254 | 0.65 | 0.82 | 34 | URI |
Interfaces
12 interfaces between chains.
- A–F · 2189 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 2159 Ų buried · 27 hydrogen bonds · protein-protein
- C–E · 2005 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1068 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 1043 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2HWU · 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 2HWU · PDBe 2HWU · UniProt P0A1F6
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