MolNFT v1 · #101654 · protein
X-ray structure of the unliganded uridine phosphorylase from yersinia pseudotuberculosis at 1.7 a resolution
4NY1: “X-ray structure of the unliganded uridine phosphorylase from yersinia pseudotuberculosis at 1.7 a resolution”. X-ray diffraction, 1 ligand (NA), 4 pockets (best druggability 0.75). MolNFT v1 #101654 on GenesisL1: 3D structure…
- PDB
- 4NY1
- Type
- protein
- Length
- 502 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridine phosphorylase
- EC
- 2.4.2.3
- UniProt
- I3NID1
- Ligands
- NA
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Uridine phosphorylase (EC 2.4.2.3) | protein | 251 | 32% helix, 28% strand | I3NID1 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 614 | 0.75 | 0.81 | 51 | empty |
| 2 | 487 | 0.72 | 0.81 | 47 | EDO |
| 3 | 75 | 0.31 | 0.73 | 20 | empty |
| 4 | 59 | 0.27 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 2109 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 4NY1 · X-ray structure of the unliganded uridine phosphorylase from Yersinia pseudotuberculosis… · 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 I3NID1
- Elsewhere: RCSB PDB 4NY1 · PDBe 4NY1 · UniProt I3NID1
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