Research workbench
Oceanobacillus iheyensis macrodomain with adpr
Analyse Oceanobacillus iheyensis macrodomain with adpr in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5L9K
- Type
- protein
- Length
- 379 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Macrod-type macrodomain
- UniProt
- Q8EP31
- Ligands
- AR6
- Pockets
- 3 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Macrod-type macrodomain | protein | 190 | 41% helix, 20% strand | Q8EP31 |
| B | Macrod-type macrodomain | protein | 189 | 41% helix, 21% strand | Q8EP31 |
Ligands and binding sites
- AR6 · [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [hydroxy-[[(2R,3S,4R,5S)-3,4,5-trihydroxyoxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
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 | 182 | 0.55 | 0.79 | 27 | AR6 |
| 2 | 190 | 0.52 | 0.78 | 28 | AR6 |
| 3 | 123 | 0.39 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 537 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5L9K · Oceanobacillus iheyensis macrodomain with adpr · the same entry in another collection · 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 Q8EP31
- Elsewhere: RCSB PDB 5L9K · PDBe 5L9K · UniProt Q8EP31
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