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Crystal structure of mouse POLY(ADP-ribose) glycohydrolase (parg) catalytic domain with ADP-hpd
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
- 4NA4
- Type
- protein
- Length
- 1,504 residues
- Chains
- 3
- 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
- A1R, IOD
- Pockets
- 18 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | POLY(ADP-ribose) glycohydrolase (EC 3.2.1.143) | protein | 505 | 39% helix, 14% strand | O88622 |
| B | POLY(ADP-ribose) glycohydrolase (EC 3.2.1.143) | protein | 494 | 38% helix, 14% strand | O88622 |
| C | POLY(ADP-ribose) glycohydrolase (EC 3.2.1.143) | protein | 505 | 39% helix, 14% strand | O88622 |
Ligands and binding sites
- A1R · 5'-O-[(S)-{[(S)-{[(2R,3R,4S)-3,4-dihydroxypyrrolidin-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy) phosphoryl]adenosine · ligand · 3 copies · chains A, B, C
- IOD · Iodide ion · ion · 5 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 957 | 0.84 | 0.85 | 94 | empty |
| 2 | 1004 | 0.77 | 0.79 | 99 | A1R, IOD |
| 3 | 413 | 0.66 | 0.79 | 39 | empty |
| 4 | 366 | 0.66 | 0.80 | 37 | empty |
| 5 | 215 | 0.66 | 0.84 | 33 | A1R |
Interfaces
3 interfaces between chains.
- B–C · 423 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 325 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 63 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 27 modified (engineered).
Compared structures
- 4NA4 · Crystal structure of mouse poly(ADP-ribose) glycohydrolase (PARG) catalytic domain with… · 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 C 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 4NA4 · PDBe 4NA4 · UniProt O88622
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