Research workbench
Changes in conformational equilibria regulate the activity of the DCP2 decapping enzyme
Analyse Changes in conformational equilibria regulate the activity of the DCP2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5N2V
- Type
- protein
- Length
- 744 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MRNA-decapping enzyme subunit 1; MRNA decapping complex subunit 2; EDC1
- EC
- 3.-.-.-
- UniProt
- Q9P805, O13828, Q10108
- Ligands
- 8NK, MG
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | MRNA-decapping enzyme subunit 1 | protein | 126 | 29% helix, 45% strand | Q9P805 |
| B, E | MRNA decapping complex subunit 2 (EC 3.-.-.-) | protein | 223 | 42% helix, 20% strand | O13828 |
| C, F | EDC1 | protein | 23 | 13% helix, 4% strand | Q10108 |
Ligands and binding sites
- 8NK · 7-methylguanosine 5'-diphosphate · ligand · 2 copies · chains B, E
- MG · Magnesium ion · metal · 6 copies · chains B, E
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 | 888 | 0.73 | 0.77 | 62 | MG, 8NK |
| 2 | 1152 | 0.72 | 0.76 | 82 | empty |
| 3 | 863 | 0.72 | 0.77 | 61 | MG, 8NK |
Interfaces
7 interfaces between chains.
- A–B · 941 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 922 Ų buried · 10 hydrogen bonds · protein-protein
- D–F · 825 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 798 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 595 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5N2V · Changes in conformational equilibria regulate the activity of the Dcp2 decapping enzyme · the same entry in another collection · chain F against F, TM-score 1.00
- Q9P805 · AlphaFold monomer V2.0 prediction for mRNA-decapping enzyme subunit 1 (Q9P805) · a predicted model of the same protein · chain A against A, TM-score 0.97
- O13828 · AlphaFold monomer V2.0 prediction for mRNA decapping complex subunit 2 (O13828) · a predicted model of the same protein · chain B against A, TM-score 0.96
- Q10108 · AlphaFold monomer V2.0 prediction for uncharacterized protein C18G6.09C (Q10108) · a predicted model of the same protein · chain C against A, TM-score 0.35
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 Q9P805
- Every structure of UniProt O13828
- Every structure of UniProt Q10108
- Elsewhere: RCSB PDB 5N2V · PDBe 5N2V · UniProt Q9P805 · UniProt O13828 · UniProt Q10108
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