Research workbench
Crystal structure of S. pombe DCP2:DCP1 mRNA decapping complex
Analyse Crystal structure of S. pombe DCP2:DCP1 mRNA decapping complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5J3Y
- Type
- protein
- Length
- 729 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MRNA-decapping enzyme subunit 1; MRNA decapping complex subunit 2
- EC
- 3.6.1.62
- UniProt
- Q9P805, O13828
- Pockets
- 11 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MRNA-decapping enzyme subunit 1 | protein | 126 | 24% helix, 45% strand | Q9P805 |
| B | MRNA decapping complex subunit 2 (EC 3.6.1.62) | protein | 242 | 43% helix, 18% strand | O13828 |
| C | MRNA-decapping enzyme subunit 1 | protein | 124 | 26% helix, 46% strand | Q9P805 |
| D | MRNA decapping complex subunit 2 (EC 3.6.1.62) | protein | 237 | 39% helix, 17% strand | O13828 |
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 414 | 0.59 | 0.75 | 48 | empty |
| 2 | 424 | 0.58 | 0.75 | 47 | empty |
| 3 | 179 | 0.42 | 0.73 | 25 | empty |
| 4 | 60 | 0.38 | 0.79 | 15 | empty |
| 5 | 96 | 0.37 | 0.75 | 14 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1128 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 874 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 617 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 92 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5J3Y · Crystal structure of S. pombe Dcp2:Dcp1 mRNA decapping complex · the same entry in another collection · chain D against D, 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 C 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 D against A, TM-score 0.61
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 5J3Y · PDBe 5J3Y · UniProt Q9P805 · UniProt O13828
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