Research workbench
PanDDA analysis group deposition -- Crystal Structure of DCP2 (NUDT20) in complex with Z100435060
Analyse PanDDA analysis group deposition -- Crystal Structure of DCP2 (NUDT20) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5QP9
- Type
- protein
- Length
- 149 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.72
- Source
- Homo sapiens
- Molecule
- DCP2 (NUDT20)
- EC
- 3.6.1.62
- UniProt
- Q8IU60
- Ligands
- LJD
- Pockets
- 2 · best druggability 0.52
Structure
x-ray diffraction · resolution 1.72 · 1 distinct chain · 24% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DCP2 (NUDT20) (EC 3.6.1.62) | protein | 149 | 24% helix, 27% strand | Q8IU60 |
Ligands and binding sites
- LJD · N-[(4-chlorophenyl)methyl]-1-methyl-1H-pyrazole-4-carboxamide · ligand · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
- ACT · Acetate ion · additive · 2 copies · chains A
- DMS · Dimethyl sulfoxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 146 | 0.52 | 0.80 | 25 | LJD |
| 2 | 52 | 0.31 | 0.76 | 11 | empty |
Compared structures
- 5QP9 · Pandda analysis group deposition -- crystal structure of DCP2 (NUDT20) in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8IU60 · AlphaFold monomer V2.0 prediction for M7GPPPN-mRNA hydrolase (Q8IU60) · a predicted model of the same protein · chain A against A, TM-score 0.90
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 Q8IU60
- Elsewhere: RCSB PDB 5QP9 · PDBe 5QP9 · UniProt Q8IU60
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