MolNFT v1 · #95957 · protein
TARG1 (C6ORF130), terminal ADP-ribose glycohydrolase 1 bound to ADP- hpd
4J5R · O-acetyl-ADP-ribose deacetylase 1: “TARG1 (C6ORF130), terminal ADP-ribose glycohydrolase 1 bound to ADP- hpd”. X-ray diffraction, 2 ligands (A1R, CL), 3 pockets (best druggability 0.60). MolNFT v1 #95957 on GenesisL1: 3D structure…
- PDB
- 4J5R
- Type
- protein
- Length
- 280 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-acetyl-ADP-ribose deacetylase 1
- EC
- 3.5.1.-
- UniProt
- Q9Y530
- Ligands
- A1R, CL
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | O-acetyl-ADP-ribose deacetylase 1 (EC 3.5.1.-) | protein | 141 | 34% helix, 27% strand | Q9Y530 |
| B | O-acetyl-ADP-ribose deacetylase 1 (EC 3.5.1.-) | protein | 139 | 32% helix, 26% strand | Q9Y530 |
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 · 2 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 216 | 0.60 | 0.81 | 33 | A1R, CL |
| 2 | 171 | 0.59 | 0.82 | 25 | A1R, CL |
| 3 | 64 | 0.31 | 0.75 | 17 | EDO |
Interfaces
1 interface between chains.
- A–B · 452 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4J5R · TARG1 (C6orf130), Terminal ADP-ribose Glycohydrolase 1 bound to ADP-HPD · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y530 · AlphaFold monomer V2.0 prediction for ADP-ribose glycohydrolase OARD1 (Q9Y530) · a predicted model of the same protein · chain B 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 Q9Y530
- Elsewhere: RCSB PDB 4J5R · PDBe 4J5R · UniProt Q9Y530
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