Research workbench
Oryza sativa apl macrodomain in complex with ADP-ribose
Analyse Oryza sativa apl macrodomain in complex with ADP-ribose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LW0
- Type
- protein
- Length
- 406 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Basic helix-loop-helix, putative, expressed
- UniProt
- Q10MW4
- Ligands
- AR6, GLY, PO4
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Basic helix-loop-helix, putative, expressed | protein | 202 | 41% helix, 17% strand | Q10MW4 |
| B | Basic helix-loop-helix, putative, expressed | protein | 204 | 41% helix, 16% strand | Q10MW4 |
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
- GLY · Glycine · ligand · 2 copies · chains B
- PO4 · Phosphate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 508 | 0.73 | 0.82 | 55 | empty |
| 2 | 231 | 0.61 | 0.81 | 40 | AR6 |
| 3 | 177 | 0.61 | 0.83 | 32 | AR6 |
| 4 | 131 | 0.44 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 652 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5LW0 · Oryza sativa APL macrodomain in complex with ADP-ribose · 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 Q10MW4
- Elsewhere: RCSB PDB 5LW0 · PDBe 5LW0 · UniProt Q10MW4
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