MolNFT v1 · #86274 · protein
Structure of human parg catalytic domain in complex with ADP-hpd
4B1J · POLY(ADP-ribose) glycohydrolase: “Structure of human parg catalytic domain in complex with ADP-hpd”. X-ray diffraction, 2 ligands (A1R, SO4), 6 pockets (best druggability 0.68). MolNFT v1 #86274 on GenesisL1: 3D structure, binding…
- PDB
- 4B1J
- Type
- protein
- Length
- 508 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- POLY(ADP-ribose) glycohydrolase
- EC
- 3.2.1.143
- UniProt
- Q86W56
- Ligands
- A1R, SO4
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | POLY(ADP-ribose) glycohydrolase (EC 3.2.1.143) | protein | 508 | 40% helix, 16% strand | Q86W56 |
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 · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 455 | 0.68 | 0.80 | 43 | empty |
| 2 | 197 | 0.66 | 0.85 | 34 | A1R |
| 3 | 92 | 0.44 | 0.78 | 12 | GOL |
| 4 | 89 | 0.38 | 0.77 | 16 | empty |
| 5 | 75 | 0.34 | 0.76 | 21 | empty |
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 4B1J · Structure of human PARG catalytic domain in complex with ADP-HPD · the same entry in another collection · chain A against A, TM-score 1.00
- Q86W56 · AlphaFold monomer V2.0 prediction for POLY(ADP-ribose) glycohydrolase (Q86W56) · a predicted model of the same protein · 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 Q86W56
- Elsewhere: RCSB PDB 4B1J · PDBe 4B1J · UniProt Q86W56
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