MolNFT v1 · #29841 · protein
Crystal structure of the uridine phosphorylase from salmonella typhimurium in complex with 2,2'-anhydrouridine and phosphate ion at 1.85A resolution
1ZL2: “Crystal structure of the uridine phosphorylase from salmonella typhimurium in complex with…”. X-ray diffraction, 2 ligands (ANU, PO4), 17 pockets (best druggability 0.71). MolNFT v1 #29841 on GenesisL1: 3D structure, binding sites…
- PDB
- 1ZL2
- Type
- protein
- Length
- 1,460 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridine phosphorylase
- EC
- 2.4.2.3
- UniProt
- O33808
- Ligands
- ANU, PO4
- Pockets
- 17 · best druggability 0.71
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 | 253 | 32% helix, 28% strand | O33808 |
| B | Uridine phosphorylase (EC 2.4.2.3) | protein | 242 | 31% helix, 30% strand | O33808 |
| C | Uridine phosphorylase (EC 2.4.2.3) | protein | 243 | 34% helix, 28% strand | O33808 |
| D | Uridine phosphorylase (EC 2.4.2.3) | protein | 241 | 34% helix, 30% strand | O33808 |
| E | Uridine phosphorylase (EC 2.4.2.3) | protein | 241 | 34% helix, 30% strand | O33808 |
| F | Uridine phosphorylase (EC 2.4.2.3) | protein | 240 | 33% helix, 30% strand | O33808 |
Ligands and binding sites
- ANU · 2,2'-Anhydro-(1-beta-D-arabinofuranosyl)uracil · ligand · 3 copies · chains B, D, A, F
- PO4 · Phosphate ion · ion · 3 copies · chains B, D, A, F
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 | 412 | 0.71 | 0.82 | 38 | empty |
| 2 | 436 | 0.70 | 0.81 | 46 | empty |
| 3 | 417 | 0.69 | 0.80 | 48 | empty |
| 4 | 406 | 0.68 | 0.81 | 43 | empty |
| 5 | 323 | 0.65 | 0.80 | 34 | empty |
Interfaces
12 interfaces between chains.
- B–D · 2133 Ų buried · 27 hydrogen bonds · protein-protein
- A–F · 2091 Ų buried · 28 hydrogen bonds · protein-protein
- C–E · 1959 Ų buried · 29 hydrogen bonds · protein-protein
- A–E · 1031 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 1025 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1ZL2 · 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 O33808
- Elsewhere: RCSB PDB 1ZL2 · PDBe 1ZL2 · UniProt O33808
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