MolNFT v1 · #95958 · protein
TARG1 (C6ORF130), terminal ADP-ribose glycohydrolase 1 ADP-ribose complex
4J5S · O-acetyl-ADP-ribose deacetylase 1: “TARG1 (C6ORF130), terminal ADP-ribose glycohydrolase 1 ADP-ribose complex”. X-ray diffraction, 4 ligands (ZZC, SBE, CL), 14 pockets (best druggability 0.62). MolNFT v1 #95958 on GenesisL1: 3D…
- PDB
- 4J5S
- Type
- protein
- Length
- 567 residues
- Chains
- 4
- 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
- ZZC, SBE, CL, BO4
- Pockets
- 14 · best druggability 0.62
Structure
x-ray diffraction · 3 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 | 146 | 32% helix, 25% strand | Q9Y530 |
| B | O-acetyl-ADP-ribose deacetylase 1 (EC 3.5.1.-) | protein | 141 | 33% helix, 27% strand | Q9Y530 |
| C, D | O-acetyl-ADP-ribose deacetylase 1 (EC 3.5.1.-) | protein | 140 | 34% helix, 24% strand | Q9Y530 |
Ligands and binding sites
- ZZC · [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [[(2R,3R)-2,3-dihydroxy-4-oxo-pentoxy]-oxido-phosphoryl] phosphate · ligand · 4 copies · chains A, B, C, D
- SBE · 1,3,2-dioxaborolan-2-ol · ligand · chains B
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- BO4 · Borate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 19 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 253 | 0.62 | 0.81 | 31 | ZZC, CL |
| 2 | 226 | 0.60 | 0.81 | 34 | ZZC, CL |
| 3 | 211 | 0.59 | 0.80 | 31 | ZZC, CL |
| 4 | 204 | 0.59 | 0.80 | 34 | ZZC, CL |
| 5 | 137 | 0.51 | 0.80 | 25 | EDO |
Interfaces
4 interfaces between chains.
- A–C · 393 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 387 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 386 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 376 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 4J5S · TARG1 (C6orf130), Terminal ADP-ribose Glycohydrolase 1 ADP-ribose complex · 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 C 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 4J5S · PDBe 4J5S · UniProt Q9Y530
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