MolNFT v1 · #168795 · protein + RNA
Crystal structure of mouse dxo in complex with 5'-oh RNA substrate mimic and calcium ion
6WRE · Decapping and exoribonuclease protein: “Crystal structure of mouse dxo in complex with 5'-oh RNA substrate mimic and calcium ion”. X-ray diffraction, 2 ligands (U3P, CA), 3 pockets (best druggability 0.79). MolNFT v1 #168795 on…
- PDB
- 6WRE
- Type
- protein + RNA
- Length
- 362 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Decapping and exoribonuclease protein; RNA (5'-R(*UP*(U37)P*(U37)P*UP)-3')
- EC
- 3.1.13.-, 3.6.1.-
- UniProt
- O70348
- Ligands
- U3P, CA
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Decapping and exoribonuclease protein (EC 3.1.13.-, 3.6.1.-) | protein | 358 | 30% helix, 28% strand | O70348 |
| D | RNA (5'-R(*UP*(U37)P*(U37)P*UP)-3') | rna | 4 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 764 | 0.79 | 0.83 | 62 | empty |
| 2 | 194 | 0.61 | 0.83 | 30 | empty |
| 3 | 60 | 0.29 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–D · 753 Ų buried · 20 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 6WRE · Crystal structure of mouse DXO in complex with 5'-OH RNA substrate mimic and calcium ion · the same entry in another collection · chain A against A, TM-score 1.00
- O70348 · AlphaFold monomer V2.0 prediction for decapping and exoribonuclease protein (O70348) · a predicted model of the same protein · 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 O70348
- Elsewhere: RCSB PDB 6WRE · PDBe 6WRE · UniProt O70348
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