MolNFT v1 · #49322 · protein
The crystal structure of fission yeast mRNA decapping enzyme DCP1-DCP2 complex
2QKL · SPBC3B9.21 protein: “The crystal structure of fission yeast mRNA decapping enzyme DCP1-DCP2 complex”. X-ray diffraction, 1 ligand (PB), 2 pockets (best druggability 0.32). MolNFT v1 #49322 on GenesisL1: 3D structure, binding sites…
- PDB
- 2QKL
- Type
- protein
- Length
- 211 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SPBC3B9.21 protein; SPAC19A8.12 protein
- EC
- 3.6.1.30
- UniProt
- Q9P805, O13828
- Ligands
- PB
- Pockets
- 2 · best druggability 0.32
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SPBC3B9.21 protein | protein | 121 | 27% helix, 46% strand | Q9P805 |
| B | SPAC19A8.12 protein (EC 3.6.1.30) | protein | 90 | 67% helix, 0% strand | O13828 |
Ligands and binding sites
- PB · Lead (II) ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.32 | 0.74 | 20 | empty |
| 2 | 53 | 0.30 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1059 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 2QKL · The crystal structure of fission yeast mRNA decapping enzyme Dcp1-Dcp2 complex · the same entry in another collection · chain A against A, 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 0.95
- 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 0.85
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
- Elsewhere: RCSB PDB 2QKL · PDBe 2QKL · UniProt Q9P805 · UniProt O13828
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