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Crystal structure of purine nucleoside phosphorylase I from spirosoma linguale dsm 74, nysgrc target 029362
Analyse Crystal structure of purine nucleoside phosphorylase I from spirosoma linguale… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LNA
- Type
- protein
- Length
- 269 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purine nucleoside phosphorylase
- EC
- 2.4.2.1
- UniProt
- D2QIK7
- Ligands
- ADE, PO4, CL
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 269 | 36% helix, 24% strand | D2QIK7 |
Ligands and binding sites
- ADE · Adenine · ligand · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains A
- CL · Chloride ion · ion · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · 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 | 187 | 0.67 | 0.86 | 27 | PO4, ADE, MPD |
| 2 | 160 | 0.54 | 0.80 | 30 | empty |
| 3 | 79 | 0.34 | 0.75 | 18 | empty |
| 4 | 68 | 0.31 | 0.75 | 17 | empty |
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 4LNA · CRYSTAL STRUCTURE OF purine nucleoside phosphorylase I from Spirosoma linguale DSM 74… · 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 D2QIK7
- Elsewhere: RCSB PDB 4LNA · PDBe 4LNA · UniProt D2QIK7
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