Research workbench
Structure of human ARH3 D314E bound to ADP-ribose and magnesium
Analyse Structure of human ARH3 D314E bound to ADP-ribose and magnesium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D3A
- Type
- protein
- Length
- 1,354 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- POLY(ADP-ribose) glycohydrolase ARH3
- EC
- 3.2.1.143
- UniProt
- Q9NX46
- Ligands
- AR6, MG
- Pockets
- 15 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 66% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | POLY(ADP-ribose) glycohydrolase ARH3 (EC 3.2.1.143) | protein | 341 | 67% helix, 2% strand | Q9NX46 |
| D | POLY(ADP-ribose) glycohydrolase ARH3 (EC 3.2.1.143) | protein | 334 | 66% helix, 1% strand | Q9NX46 |
| A | POLY(ADP-ribose) glycohydrolase ARH3 (EC 3.2.1.143) | protein | 347 | 64% helix, 1% strand | Q9NX46 |
| B | POLY(ADP-ribose) glycohydrolase ARH3 (EC 3.2.1.143) | protein | 332 | 68% helix, 1% strand | Q9NX46 |
Ligands and binding sites
- AR6 · [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [hydroxy-[[(2R,3S,4R,5S)-3,4,5-trihydroxyoxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate · ligand · 4 copies · chains C, D, A, B
- MG · Magnesium ion · metal · 4 copies · chains C, D, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 307 | 0.77 | 0.88 | 52 | empty |
| 2 | 364 | 0.76 | 0.86 | 57 | empty |
| 3 | 64 | 0.73 | 0.98 | 20 | empty |
| 4 | 57 | 0.73 | 0.99 | 21 | empty |
| 5 | 58 | 0.72 | 0.99 | 22 | empty |
Interfaces
2 interfaces between chains.
- A–B · 946 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 918 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6D3A · Structure of human ARH3 D314E bound to ADP-ribose and magnesium · the same entry in another collection · chain B against B, TM-score 1.00
- Q9NX46 · AlphaFold monomer V2.0 prediction for ADP-ribose glycohydrolase ARH3 (Q9NX46) · 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 Q9NX46
- Elsewhere: RCSB PDB 6D3A · PDBe 6D3A · UniProt Q9NX46
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