Research workbench
Oceanobacillus iheyensis macrodomain with mes bound
Analyse Oceanobacillus iheyensis macrodomain with mes bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FUD
- Type
- protein
- Length
- 379 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-acetyl-ADP-ribose deacetylase
- EC
- 3.2.2.-, 3.5.1.-
- UniProt
- Q8EP31
- Ligands
- SO4, CL
- Pockets
- 2 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | O-acetyl-ADP-ribose deacetylase (EC 3.2.2.-, 3.5.1.-) | protein | 189 | 41% helix, 21% strand | Q8EP31 |
| B | O-acetyl-ADP-ribose deacetylase (EC 3.2.2.-, 3.5.1.-) | protein | 190 | 39% helix, 21% strand | Q8EP31 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 116 | 0.51 | 0.81 | 25 | MES |
| 2 | 108 | 0.49 | 0.81 | 20 | MES |
Interfaces
1 interface between chains.
- A–B · 552 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5FUD · Oceanobacillus iheyensis macrodomain with MES bound · 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 5FUD · PDBe 5FUD · UniProt Q8EP31
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