MolNFT v1 · #122914 · protein
Crystal structure of S. pombe DCP2:DCP1:EDC1 mRNA decapping complex
5J3T · MRNA-decapping enzyme subunit 1: “Crystal structure of S. pombe DCP2:DCP1:EDC1 mRNA decapping complex”. X-ray diffraction, 1 ligand (MG), 4 pockets (best druggability 0.54). MolNFT v1 #122914 on GenesisL1: 3D structure, binding…
- PDB
- 5J3T
- Type
- protein
- Length
- 381 residues
- Chains
- 3
- 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
- 3.6.1.62
- UniProt
- Q9P805, O13828, Q10108
- Ligands
- MG
- Pockets
- 4 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MRNA-decapping enzyme subunit 1 | protein | 126 | 25% helix, 48% strand | Q9P805 |
| B | MRNA decapping complex subunit 2 (EC 3.6.1.62) | protein | 230 | 43% helix, 16% strand | O13828 |
| C | EDC1 | protein | 25 | 24% helix, 16% strand | Q10108 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 230 | 0.54 | 0.77 | 31 | empty |
| 2 | 178 | 0.47 | 0.76 | 30 | FMT |
| 3 | 151 | 0.47 | 0.77 | 22 | empty |
| 4 | 133 | 0.40 | 0.74 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 842 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 834 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 711 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5J3T · Crystal structure of S. pombe Dcp2:Dcp1:Edc1 mRNA decapping 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 0.93
- 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 0.59
- 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 0.20
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 5J3T · PDBe 5J3T · UniProt Q9P805 · UniProt O13828 · UniProt Q10108
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