Research workbench
Escherichia COLI purine nucleoside phosphorylase complexed with 7- deazaadenosine and PHOSPHATE/SULFATE
Analyse Escherichia COLI purine nucleoside phosphorylase complexed with 7… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PR5
- Type
- protein
- Length
- 701 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
- P0ABP9
- Ligands
- TBN, PO4
- Pockets
- 7 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Purine nucleoside phosphorylase deod-type (EC 2.4.2.1) | protein | 231 | 35% helix, 28% strand | P0ABP9 |
| B | Purine nucleoside phosphorylase deod-type (EC 2.4.2.1) | protein | 233 | 36% helix, 28% strand | P0ABP9 |
| C | Purine nucleoside phosphorylase deod-type (EC 2.4.2.1) | protein | 237 | 33% helix, 28% strand | P0ABP9 |
Ligands and binding sites
- TBN · 2-(4-amino-pyrrolo[2,3-d]pyrimidin-7-yl)-5-hydroxymethyl-tetrahydro-furan-3,4-diol · ligand · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 237 | 0.58 | 0.79 | 37 | PO4, TBN |
| 2 | 270 | 0.57 | 0.77 | 43 | PO4, TBN |
| 3 | 301 | 0.56 | 0.76 | 48 | PO4, TBN |
| 4 | 125 | 0.37 | 0.73 | 18 | empty |
| 5 | 65 | 0.34 | 0.77 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 140 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 118 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 107 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1PR5 · Escherichia coli Purine Nucleoside Phosphorylase Complexed with 7-deazaadenosine and… · the same entry in another collection · chain A against A, TM-score 1.00
- P0ABP9 · AlphaFold monomer V2.0 prediction for purine nucleoside phosphorylase deod-type (P0ABP9) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P0ABP9
- Elsewhere: RCSB PDB 1PR5 · PDBe 1PR5 · UniProt P0ABP9
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