Research workbench
Crystal structure of mouse POLY(ADP-ribose) glycohydrolase (parg) catalytic domain
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
- 4FC2
- Type
- protein
- Length
- 2,031 residues
- Chains
- 4
- 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
- SO4
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | POLY(ADP-ribose) glycohydrolase (EC 3.2.1.143) | protein | 508 | 40% helix, 14% strand | O88622 |
| B | POLY(ADP-ribose) glycohydrolase (EC 3.2.1.143) | protein | 507 | 40% helix, 14% strand | O88622 |
| D | POLY(ADP-ribose) glycohydrolase (EC 3.2.1.143) | protein | 508 | 40% helix, 14% strand | O88622 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 28 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 416 | 0.74 | 0.84 | 44 | empty |
| 2 | 323 | 0.73 | 0.86 | 33 | empty |
| 3 | 418 | 0.73 | 0.84 | 42 | empty |
| 4 | 393 | 0.69 | 0.81 | 41 | empty |
| 5 | 391 | 0.69 | 0.81 | 41 | empty |
Interfaces
4 interfaces between chains.
- A–D · 539 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 204 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 178 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 38 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified (engineered).
Compared structures
- 4FC2 · Crystal structure of mouse poly(ADP-ribose) glycohydrolase (PARG) catalytic domain · the same entry in another collection · chain C against C, 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 4FC2 · PDBe 4FC2 · UniProt O88622
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