Research workbench
Crystal structure of M. tuberculosis pnp in complex with iminoribitol, 9-deazahypoxanthine and phosphate ion
Analyse Crystal structure of M. tuberculosis pnp in complex with iminoribitol… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1I80
- Type
- protein
- Length
- 791 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
- P0A538
- Ligands
- 9HX, IMR, PO4
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 266 | 35% helix, 23% strand | P0A538 |
| B | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 263 | 35% helix, 24% strand | P0A538 |
| C | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 262 | 36% helix, 24% strand | P0A538 |
Ligands and binding sites
- 9HX · 9-deazahypoxanthine · ligand · 3 copies · chains A, B, C
- IMR · Iminoribitol · ligand · chains A, B
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 325 | 0.84 | 0.94 | 46 | empty |
| 2 | 870 | 0.73 | 0.78 | 127 | empty |
| 3 | 227 | 0.64 | 0.83 | 41 | 9HX |
| 4 | 213 | 0.64 | 0.83 | 46 | PO4, 9HX, IMR |
| 5 | 239 | 0.63 | 0.82 | 38 | 9HX |
Interfaces
3 interfaces between chains.
- A–C · 974 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 933 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 932 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1I80 · Crystal structure of M. tuberculosis pnp in complex with iminoribitol… · 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 P0A538
- Elsewhere: RCSB PDB 1I80 · PDBe 1I80 · UniProt P0A538
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