Research workbench
Crystal structure of POLY(ADP-ribose) glycohydrolase (parg) from deinococcus radiodurans in complex with ADP-ribose (P21)
Analyse Crystal structure of POLY(ADP-ribose) glycohydrolase (parg) from deinococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZDB
- Type
- protein
- Length
- 504 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Poly ADP-ribose glycohydrolase
- UniProt
- Q9RZM4
- Ligands
- AR6
- Pockets
- 2 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Poly ADP-ribose glycohydrolase | protein | 253 | 47% helix, 19% strand | Q9RZM4 |
| B | Poly ADP-ribose glycohydrolase | protein | 251 | 46% helix, 19% strand | Q9RZM4 |
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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 815 | 0.79 | 0.82 | 92 | AR6 |
| 2 | 394 | 0.69 | 0.81 | 56 | AR6 |
Interfaces
1 interface between chains.
- A–B · 771 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5ZDB · Crystal structure of poly(ADP-ribose) glycohydrolase (PARG) from Deinococcus radiodurans… · 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 Q9RZM4
- Elsewhere: RCSB PDB 5ZDB · PDBe 5ZDB · UniProt Q9RZM4
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