MolNFT v1 · #138450 · protein
Crystal structure of the F61S mutant of HSNUDT16
5WJI · U8 snorna-decapping enzyme: “Crystal structure of the F61S mutant of HSNUDT16”. X-ray diffraction, 2 ligands (CL, SO4), 3 pockets (best druggability 0.75). MolNFT v1 #138450 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5WJI
- Type
- protein
- Length
- 350 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- U8 snorna-decapping enzyme
- EC
- 3.6.1.62, 3.6.1.64
- UniProt
- Q96DE0
- Ligands
- CL, SO4
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | U8 snorna-decapping enzyme (EC 3.6.1.62, 3.6.1.64) | protein | 176 | 32% helix, 34% strand | Q96DE0 |
| B | U8 snorna-decapping enzyme (EC 3.6.1.62, 3.6.1.64) | protein | 174 | 29% helix, 34% strand | Q96DE0 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A
- SO4 · Sulfate ion · ion · chains A
- ACY · Acetic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 78 | 0.75 | 0.98 | 23 | empty |
| 2 | 233 | 0.53 | 0.77 | 30 | empty |
| 3 | 170 | 0.46 | 0.76 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1346 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
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 Q96DE0
- Elsewhere: RCSB PDB 5WJI · PDBe 5WJI · UniProt Q96DE0
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