Research workbench
Asymmetric trimer of the drosophila melanogaster DCP1 C- terminal domain
Analyse Asymmetric trimer of the drosophila melanogaster DCP1 C- terminal domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WX4
- Type
- protein
- Length
- 255 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Decapping protein 1
- UniProt
- Q9W1H5
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.63
Structure
x-ray diffraction · 6 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Decapping protein 1 | protein | 38 | 71% helix, 0% strand | Q9W1H5 |
| B | Decapping protein 1 | protein | 41 | 80% helix, 0% strand | Q9W1H5 |
| C | Decapping protein 1 | protein | 43 | 81% helix, 0% strand | Q9W1H5 |
| D | Decapping protein 1 | protein | 45 | 73% helix, 0% strand | Q9W1H5 |
| E | Decapping protein 1 | protein | 43 | 86% helix, 0% strand | Q9W1H5 |
| F | Decapping protein 1 | protein | 45 | 82% helix, 0% strand | Q9W1H5 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, D, E, C, F
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 | 417 | 0.63 | 0.77 | 44 | SO4 |
| 2 | 88 | 0.37 | 0.76 | 15 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1027 Ų buried · 2 hydrogen bonds · protein-protein
- D–E · 957 Ų buried · 4 hydrogen bonds · protein-protein
- E–F · 911 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 822 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 793 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2WX4 · Asymmetric trimer of the Drosophila melanogaster DCP1 C-terminal domain · 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 Q9W1H5
- Elsewhere: RCSB PDB 2WX4 · PDBe 2WX4 · UniProt Q9W1H5
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