MolNFT v1 · #142890 · protein
Crystal structure of dxo (E234A mutant) in complex with adenosine 3', 5' bisphosphate and two magnesium ions
6AIY · Decapping and exoribonuclease protein: “Crystal structure of dxo (E234A mutant) in complex with adenosine 3', 5' bisphosphate and two magnesium ions”. X-ray diffraction, 2 ligands (A3P, MG), 3 pockets (best druggability 0.77).…
- PDB
- 6AIY
- Type
- protein
- Length
- 358 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Decapping and exoribonuclease protein
- EC
- 3.1.13.-, 3.6.1.-
- UniProt
- O70348
- Ligands
- A3P, MG
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 29% 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, 29% strand | O70348 |
Ligands and binding sites
- A3P · Adenosine-3'-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 898 | 0.77 | 0.80 | 71 | A3P, MG |
| 2 | 68 | 0.34 | 0.76 | 15 | empty |
| 3 | 55 | 0.29 | 0.75 | 15 | empty |
Compared structures
- 6AIY · Crystal structure of DXO (E234A mutant) in complex with adenosine 3', 5' bisphosphate and… · 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 6AIY · PDBe 6AIY · UniProt O70348
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