Research workbench
Crystal structure of dxo in complex with adenosine 3', 5' bisphosphate and two magnesium ions
Analyse Crystal structure of dxo in complex with adenosine 3', 5' bisphosphate and two… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AIX
- 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 0.76
Structure
x-ray diffraction · 1 distinct chain · 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 |
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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1104 | 0.76 | 0.78 | 60 | A3P, MG |
| 2 | 174 | 0.53 | 0.79 | 29 | empty |
| 3 | 57 | 0.31 | 0.76 | 18 | empty |
Compared structures
- 6AIX · Crystal structure of DXO in complex with adenosine 3', 5' bisphosphate and two magnesium… · 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 6AIX · PDBe 6AIX · UniProt O70348
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