MolNFT v1 · #98582 · protein
Crystal structure of a putative purine nucleoside phosphorylase from vibrio fischeri ES114 (target nysgrc-029521)
4LDN · Purine nucleoside phosphorylase deod-type: “Crystal structure of a putative purine nucleoside phosphorylase from vibrio fischeri ES114 (target…”. X-ray diffraction, 1 ligand (PO4), 3 pockets (best druggability 0.57). MolNFT v1…
- PDB
- 4LDN
- Type
- protein
- Length
- 244 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purine nucleoside phosphorylase deod-type
- EC
- 2.4.2.1
- UniProt
- Q5DYV8
- Ligands
- PO4
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Purine nucleoside phosphorylase deod-type (EC 2.4.2.1) | protein | 244 | 36% helix, 28% strand | Q5DYV8 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 277 | 0.57 | 0.77 | 31 | PO4 |
| 2 | 51 | 0.43 | 0.84 | 15 | empty |
| 3 | 59 | 0.29 | 0.75 | 16 | empty |
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 4LDN · Crystal structure of a putative purine nucleoside phosphorylase from Vibrio fischeri… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5DYV8 · AlphaFold monomer V2.0 prediction for purine nucleoside phosphorylase deod-type (Q5DYV8) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q5DYV8
- Elsewhere: RCSB PDB 4LDN · PDBe 4LDN · UniProt Q5DYV8
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