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Crystal structure of mouse POLY(ADP-ribose) glycohydrolase (parg) catalytic domain mutant E749Q
Analyse Crystal structure of mouse POLY(ADP-ribose) glycohydrolase (parg) catalytic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4N9Z
- Type
- protein
- Length
- 1,017 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- POLY(ADP-ribose) glycohydrolase
- EC
- 3.2.1.143
- UniProt
- O88622
- Ligands
- V3L, SO4
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | POLY(ADP-ribose) glycohydrolase (EC 3.2.1.143) | protein | 509 | 39% helix, 15% strand | O88622 |
| B | POLY(ADP-ribose) glycohydrolase (EC 3.2.1.143) | protein | 508 | 40% helix, 14% strand | O88622 |
Ligands and binding sites
- V3L · 2'-O-(5-O-phosphono-alpha-D-ribofuranosyl)adenosine 5'-(dihydrogen phosphate) · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 820 | 0.79 | 0.83 | 77 | empty |
| 2 | 675 | 0.73 | 0.80 | 54 | empty |
| 3 | 391 | 0.73 | 0.83 | 43 | empty |
| 4 | 158 | 0.55 | 0.80 | 33 | empty |
| 5 | 168 | 0.53 | 0.79 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 462 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4N9Z · Crystal structure of mouse poly(ADP-ribose) glycohydrolase (PARG) catalytic domain mutant… · the same entry in another collection · chain A against A, TM-score 1.00
- O88622 · AlphaFold monomer V2.0 prediction for POLY(ADP-ribose) glycohydrolase (O88622) · a predicted model of the same protein · chain B 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 O88622
- Elsewhere: RCSB PDB 4N9Z · PDBe 4N9Z · UniProt O88622
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