MolNFT v1 · #151219 · protein
ADP-ribosylserine hydrolase ARH3 of latimeria chalumnae in complex with ADP-ribose
6HGZ · ADP-ribosylhydrolase like 2: “ADP-ribosylserine hydrolase ARH3 of latimeria chalumnae in complex with ADP-ribose”. X-ray diffraction, 2 ligands (AR6, MG), 4 pockets (best druggability 0.87). MolNFT v1 #151219 on GenesisL1: 3D…
- PDB
- 6HGZ
- Type
- protein
- Length
- 654 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosylhydrolase like 2
- UniProt
- H3BCW1
- Ligands
- AR6, MG
- Pockets
- 4 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 68% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ADP-ribosylhydrolase like 2 | protein | 327 | 68% helix, 1% strand | H3BCW1 |
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 · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1017 | 0.87 | 0.88 | 115 | AR6 |
| 2 | 55 | 0.46 | 0.84 | 16 | empty |
| 3 | 101 | 0.44 | 0.78 | 22 | empty |
| 4 | 63 | 0.32 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 795 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6HGZ · ADP-ribosylserine hydrolase ARH3 of Latimeria chalumnae in complex with ADP-ribose · the same entry in another collection · chain A against A, TM-score 1.00
- H3BCW1 · AlphaFold monomer V2.0 prediction for ADP-ribose glycohydrolase ARH3 (H3BCW1) · 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 H3BCW1
- Elsewhere: RCSB PDB 6HGZ · PDBe 6HGZ · UniProt H3BCW1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.