MolNFT v1 · #67583 · protein
Crystal structure of purine nucleoside phosphorylase from mycobacterium tuberculosis in complex with 2'-deoxyguanosine
3IOM: “Crystal structure of purine nucleoside phosphorylase from mycobacterium tuberculosis in complex with…”. X-ray diffraction, 2 ligands (GNG, SO4), 8 pockets (best druggability 0.66). MolNFT v1 #67583 on GenesisL1: 3D structure…
- PDB
- 3IOM
- Type
- protein
- Length
- 524 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purine nucleoside phosphorylase
- EC
- 2.4.2.1
- UniProt
- P0A538
- Ligands
- GNG, SO4
- Pockets
- 8 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 262 | 37% helix, 24% strand | P0A538 |
Ligands and binding sites
- GNG · 2'-deoxy-guanosine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 61 | 0.66 | 0.94 | 23 | SO4, GNG |
| 2 | 70 | 0.65 | 0.93 | 24 | SO4, GNG |
| 3 | 128 | 0.43 | 0.77 | 31 | empty |
| 4 | 114 | 0.43 | 0.78 | 27 | empty |
| 5 | 97 | 0.37 | 0.75 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 566 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3IOM · Crystal structure of Purine Nucleoside Phosphorylase from Mycobacterium tuberculosis in… · 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 3IOM · PDBe 3IOM · UniProt P0A538
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