Research workbench
Crystal structure of the human nudix hydrolase NUDT16 in complex with FAD
Analyse Crystal structure of the human nudix hydrolase NUDT16 in complex with FAD in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6X7U
- Type
- protein
- Length
- 323 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
- FAD, AMP, MN
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | U8 snorna-decapping enzyme (EC 3.6.1.62, 3.6.1.64) | protein | 162 | 28% helix, 36% strand | Q96DE0 |
| C | U8 snorna-decapping enzyme (EC 3.6.1.62, 3.6.1.64) | protein | 161 | 25% helix, 35% strand | Q96DE0 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A, C
- AMP · Adenosine monophosphate · ligand · chains C
- MN · Manganese (II) ion · metal · 4 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.73 | 0.98 | 19 | empty |
| 2 | 184 | 0.53 | 0.79 | 28 | AMP, MN |
| 3 | 197 | 0.52 | 0.78 | 25 | FAD, MN |
Interfaces
1 interface between chains.
- A–C · 1382 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6X7U · Crystal Structure of the Human Nudix Hydrolase Nudt16 in complex with FAD · 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 C against A, TM-score 0.98
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 6X7U · PDBe 6X7U · UniProt Q96DE0
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