Research workbench
Crystal structure of purine nucleoside phosphorylase from mycobacterium tuberculosis in complex with acyclovir
Analyse Crystal structure of purine nucleoside phosphorylase from mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IX2
- Type
- protein
- Length
- 786 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purine nucleoside phosphorylase
- EC
- 2.4.2.1
- UniProt
- P0A539
- Ligands
- AC2, PO4
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 262 | 32% helix, 24% strand | P0A539 |
Ligands and binding sites
- AC2 · 9-hyroxyethoxymethylguanine · 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
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 | 241 | 0.83 | 0.95 | 45 | empty |
| 2 | 648 | 0.70 | 0.78 | 97 | empty |
| 3 | 216 | 0.60 | 0.81 | 50 | PO4, AC2 |
| 4 | 226 | 0.59 | 0.80 | 45 | PO4, AC2 |
| 5 | 248 | 0.58 | 0.79 | 49 | PO4, AC2 |
Interfaces
3 interfaces between chains.
- A–B · 940 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 921 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 891 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3IX2 · Crystal structure of purine nucleoside phosphorylase from mycobacterium tuberculosis in… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A539 · AlphaFold monomer V2.0 prediction for purine nucleoside phosphorylase (P0A539) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P0A539
- Elsewhere: RCSB PDB 3IX2 · PDBe 3IX2 · UniProt P0A539
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