Research workbench
Crystal structure of human nudix motif 16 (NUDT16) in complex with imp and magnesium
Analyse Crystal structure of human nudix motif 16 (NUDT16) in complex with imp and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XSQ
- Type
- protein
- Length
- 179 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- U8 snorna-decapping enzyme
- EC
- 3.6.1.-
- UniProt
- Q96DE0
- Ligands
- IMP, MG, CL
- Pockets
- 1 · best druggability 0.54
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | U8 snorna-decapping enzyme (EC 3.6.1.-) | protein | 179 | 30% helix, 34% strand | Q96DE0 |
Ligands and binding sites
- IMP · Inosinic acid · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 234 | 0.54 | 0.77 | 30 | IMP, MG |
Compared structures
- 2XSQ · Crystal structure of human Nudix motif 16 (NUDT16) in complex with IMP and magnesium · the same entry in another collection · chain A against A, TM-score 1.00
- Q96DE0 · AlphaFold monomer V2.0 prediction for U8 snorna-decapping enzyme (Q96DE0) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 2XSQ · PDBe 2XSQ · UniProt Q96DE0
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