Research workbench
Crystal structural of MACROD1-adpr complex
Analyse Crystal structural of MACROD1-adpr complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LH4
- Type
- protein
- Length
- 940 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribose glycohydrolase MACROD1
- EC
- 3.1.1.106, 3.2.2.-
- UniProt
- Q9BQ69
- Ligands
- AR6
- Pockets
- 12 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | ADP-ribose glycohydrolase MACROD1 (EC 3.1.1.106, 3.2.2.-) | protein | 235 | 45% helix, 15% strand | Q9BQ69 |
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 · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 391 | 0.71 | 0.83 | 40 | empty |
| 2 | 632 | 0.70 | 0.78 | 60 | empty |
| 3 | 285 | 0.70 | 0.84 | 35 | AR6 |
| 4 | 227 | 0.60 | 0.81 | 38 | empty |
| 5 | 193 | 0.60 | 0.81 | 30 | AR6 |
Interfaces
3 interfaces between chains.
- A–B · 690 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 585 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 250 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
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 Q9BQ69
- Elsewhere: RCSB PDB 6LH4 · PDBe 6LH4 · UniProt Q9BQ69
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