Research workbench
Structure of human parg complexed with parg-002
Analyse Structure of human parg complexed with parg-002 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KG1
- Type
- protein
- Length
- 501 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- POLY(ADP-ribose) glycohydrolase
- EC
- 3.2.1.143
- UniProt
- Q86W56
- Ligands
- WDD, SO4
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | POLY(ADP-ribose) glycohydrolase (EC 3.2.1.143) | protein | 501 | 40% helix, 14% strand | Q86W56 |
Ligands and binding sites
- WDD · 1,3-dimethyl-8-{[2-(morpholin-4-yl)ethyl]amino}-3,7-dihydro-1H-purine-2,6-dione · ligand · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 4 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains A
- CAC · Cacodylate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 396 | 0.65 | 0.79 | 40 | SO4 |
| 2 | 184 | 0.55 | 0.79 | 30 | WDD, GOL, SO4 |
| 3 | 62 | 0.38 | 0.80 | 20 | empty |
| 4 | 85 | 0.38 | 0.76 | 12 | empty |
| 5 | 90 | 0.37 | 0.76 | 23 | DMS |
Modifications
Observed in the structure: 1 modified (artifact).
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 Q86W56
- Elsewhere: RCSB PDB 7KG1 · PDBe 7KG1 · UniProt Q86W56
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