Research workbench
Crystal structure of the catalytic domain of rat poly (ADP-ribose) glycohydrolase bound to ADP-hpd
Analyse Crystal structure of the catalytic domain of rat poly (ADP-ribose)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UEL
- Type
- protein
- Length
- 1,563 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
- Q9QYM2
- Ligands
- A1R
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | POLY(ADP-ribose) glycohydrolase (EC 3.2.1.143) | protein | 521 | 38% helix, 15% strand | Q9QYM2 |
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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 701 | 0.83 | 0.86 | 96 | empty |
| 2 | 1059 | 0.78 | 0.79 | 72 | empty |
| 3 | 423 | 0.69 | 0.80 | 37 | empty |
| 4 | 507 | 0.68 | 0.79 | 42 | empty |
| 5 | 371 | 0.67 | 0.81 | 34 | empty |
Interfaces
2 interfaces between chains.
- A–B · 569 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 334 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3UEL · Crystal structure of the catalytic domain of rat poly (ADP-ribose) glycohydrolase bound… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9QYM2 · AlphaFold monomer V2.0 prediction for POLY(ADP-ribose) glycohydrolase (Q9QYM2) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9QYM2
- Elsewhere: RCSB PDB 3UEL · PDBe 3UEL · UniProt Q9QYM2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.