Research workbench
Structural analysis of thermostable S. solfataricus purine-specific nucleoside hydrolase
Analyse Structural analysis of thermostable S. solfataricus purine-specific nucleoside… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3T8I
- Type
- protein
- Length
- 1,224 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purine nucleosidase, (iunh-2)
- EC
- 3.2.2.1
- UniProt
- Q97WH6
- Ligands
- CA
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Purine nucleosidase, (iunh-2) (EC 3.2.2.1) | protein | 306 | 44% helix, 18% strand | Q97WH6 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 17 copies · chains A, D, B, C
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains C, D
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 | 184 | 0.80 | 0.95 | 31 | GOL |
| 2 | 195 | 0.80 | 0.95 | 32 | GOL |
| 3 | 190 | 0.79 | 0.94 | 30 | CA, GOL |
| 4 | 199 | 0.79 | 0.94 | 30 | GOL |
| 5 | 429 | 0.60 | 0.75 | 60 | EDO |
Interfaces
6 interfaces between chains.
- A–D · 1256 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 1243 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 729 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 720 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 27 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3T8I · Structural analysis of thermostable S. solfataricus purine-specific nucleoside hydrolase · 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 Q97WH6
- Elsewhere: RCSB PDB 3T8I · PDBe 3T8I · UniProt Q97WH6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.