MolNFT v1 · #25336 · protein
Crystal structure of purine nucleoside phosphorylase (TM1596) from thermotoga maritima at 2.01 a resolution
1VMK: “Crystal structure of purine nucleoside phosphorylase (TM1596) from thermotoga maritima at 2.01 a resolution”. X-ray diffraction, 2 ligands (GUN, MG), 9 pockets (best druggability 0.79). MolNFT v1 #25336 on GenesisL1: 3D structure…
- PDB
- 1VMK
- Type
- protein
- Length
- 740 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
- Q9X1T2
- Ligands
- GUN, MG
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 249 | 35% helix, 27% strand | Q9X1T2 |
| B | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 250 | 36% helix, 26% strand | Q9X1T2 |
| C | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 241 | 31% helix, 28% strand | Q9X1T2 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.79 | 0.98 | 23 | empty |
| 2 | 97 | 0.79 | 0.98 | 23 | empty |
| 3 | 99 | 0.77 | 0.97 | 23 | empty |
| 4 | 361 | 0.63 | 0.78 | 43 | GUN |
| 5 | 317 | 0.60 | 0.78 | 49 | empty |
Interfaces
3 interfaces between chains.
- A–C · 985 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 979 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 961 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1VMK · Crystal structure of Purine nucleoside phosphorylase (TM1596) from Thermotoga maritima at… · 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 Q9X1T2
- Elsewhere: RCSB PDB 1VMK · PDBe 1VMK · UniProt Q9X1T2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.