MolNFT v1 · #146544 · protein
Crystal structure of arabidopsis thaliana decapping nuclease DXO1
6DKN · Decapping nuclease dxo homolog, chloroplastic: “Crystal structure of arabidopsis thaliana decapping nuclease DXO1”. X-ray diffraction, 8 pockets (best druggability 0.77). MolNFT v1 #146544 on GenesisL1: 3D structure, binding sites…
- PDB
- 6DKN
- Type
- protein
- Length
- 672 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Decapping nuclease dxo homolog, chloroplastic
- EC
- 3.6.1.-
- UniProt
- Q8RY73
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Decapping nuclease dxo homolog, chloroplastic (EC 3.6.1.-) | protein | 338 | 31% helix, 30% strand | Q8RY73 |
| B | Decapping nuclease dxo homolog, chloroplastic (EC 3.6.1.-) | protein | 334 | 32% helix, 30% strand | Q8RY73 |
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1135 | 0.77 | 0.79 | 107 | empty |
| 2 | 930 | 0.75 | 0.78 | 86 | empty |
| 3 | 130 | 0.45 | 0.77 | 21 | empty |
| 4 | 98 | 0.34 | 0.73 | 17 | empty |
| 5 | 50 | 0.31 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 559 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6DKN · Crystal structure of arabidopsis thaliana decapping nuclease DXO1 · the same entry in another collection · chain B against B, TM-score 1.00
- Q8RY73 · AlphaFold monomer V2.0 prediction for NAD-capped RNA hydrolase DXO1 (Q8RY73) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q8RY73
- Elsewhere: RCSB PDB 6DKN · PDBe 6DKN · UniProt Q8RY73
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