Research workbench
Crystal structure of wild type E. COLI purine nucleoside phosphorylase with 6 fmc molecules
Analyse Crystal structure of wild type E. COLI purine nucleoside phosphorylase with 6… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4TS9
- Type
- protein
- Length
- 711 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purine nucleoside phosphorylase deod-type
- EC
- 2.4.2.1
- UniProt
- U0SVH6
- Ligands
- FMC, PO4
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Purine nucleoside phosphorylase deod-type (EC 2.4.2.1) | protein | 237 | 36% helix, 29% strand | U0SVH6 |
Ligands and binding sites
- FMC · (1S)-1-(7-amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-D-ribitol · ligand · 3 copies · chains A, C, B
- PO4 · Phosphate ion · ion · 3 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 348 | 0.69 | 0.82 | 58 | FMC, PO4 |
| 2 | 51 | 0.68 | 0.97 | 20 | empty |
| 3 | 394 | 0.67 | 0.80 | 51 | PO4, FMC |
| 4 | 287 | 0.59 | 0.78 | 35 | empty |
| 5 | 285 | 0.58 | 0.78 | 42 | PO4, FMC |
Interfaces
3 interfaces between chains.
- B–C · 1752 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 1719 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 128 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4TS9 · Crystal structure of wild type E. Coli purine nucleoside phosphorylase with 6 FMC… · 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 U0SVH6
- Elsewhere: RCSB PDB 4TS9 · PDBe 4TS9 · UniProt U0SVH6
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