Research workbench
ADP-ribosylserine hydrolase ARH3 of latimeria chalumnae in complex with inosine diphosphate ribose (idpr)
Analyse ADP-ribosylserine hydrolase ARH3 of latimeria chalumnae in complex with inosine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HOZ
- Type
- protein
- Length
- 655 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosylhydrolase like 2
- UniProt
- H3BCW1
- Ligands
- R5I, R7I, MG
- Pockets
- 4 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 67% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ADP-ribosylhydrolase like 2 | protein | 327 | 67% helix, 2% strand | H3BCW1 |
| B | ADP-ribosylhydrolase like 2 | protein | 328 | 68% helix, 2% strand | H3BCW1 |
Ligands and binding sites
- R5I · inosine diphosphate ribose · ligand · 2 copies · chains A, B
- R7I · inosine diphosphate ribose · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- GOL · Glycerol · additive · 10 copies · chains A, B
- ACT · Acetate ion · additive · chains A, 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 | 1046 | 0.88 | 0.89 | 116 | R5I, R7I, ACT |
| 2 | 85 | 0.46 | 0.81 | 25 | empty |
| 3 | 99 | 0.42 | 0.78 | 23 | empty |
| 4 | 98 | 0.40 | 0.77 | 23 | GOL |
Interfaces
1 interface between chains.
- A–B · 805 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6HOZ · ADP-ribosylserine hydrolase ARH3 of Latimeria chalumnae in complex with inosine… · 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 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 H3BCW1
- Elsewhere: RCSB PDB 6HOZ · PDBe 6HOZ · UniProt H3BCW1
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