Research workbench
Crystal structure of E. COLI pnp complexed with PO4 and formycin a
Analyse Crystal structure of E. COLI pnp complexed with PO4 and formycin a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UT6
- 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
- P0ABP8
- Ligands
- FMC, PO4
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 35% 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 | 35% helix, 29% strand | P0ABP8 |
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 · 5 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 240 | 0.67 | 0.84 | 41 | FMC, PO4 |
| 2 | 335 | 0.67 | 0.81 | 51 | FMC, PO4 |
| 3 | 256 | 0.61 | 0.80 | 43 | FMC, PO4 |
| 4 | 264 | 0.58 | 0.78 | 32 | empty |
| 5 | 252 | 0.57 | 0.78 | 32 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1779 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 1687 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 128 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3UT6 · Crystal structure of E. Coli PNP complexed with PO4 and formycin A · the same entry in another collection · chain A against A, TM-score 1.00
- P0ABP8 · AlphaFold monomer V2.0 prediction for purine nucleoside phosphorylase deod-type (P0ABP8) · a predicted model of the same protein · 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 P0ABP8
- Elsewhere: RCSB PDB 3UT6 · PDBe 3UT6 · UniProt P0ABP8
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