MolNFT v1 · #173157 · protein
ADP-ribosylserine hydrolase ARH3 of latimeria chalumnae in complex with alpha-1''-O-methyl-ADP-ribose (meadpr)
7AQM · ADP-ribosylhydrolase like 2: “ADP-ribosylserine hydrolase ARH3 of latimeria chalumnae in complex with alpha-1''-O-methyl-ADP-ribose (meadpr)”. X-ray diffraction, 2 ligands (RVK, MG), 3 pockets (best druggability 0.87). MolNFT v1…
- PDB
- 7AQM
- Type
- protein
- Length
- 657 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosylhydrolase like 2
- EC
- 3.5.1.-, 3.2.1.143, 3.2.2.-
- UniProt
- H3BCW1
- Ligands
- RVK, MG
- Pockets
- 3 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 67% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ADP-ribosylhydrolase like 2 (EC 3.5.1.-, 3.2.1.143, 3.2.2.-) | protein | 328 | 66% helix, 1% strand | H3BCW1 |
| B | ADP-ribosylhydrolase like 2 (EC 3.5.1.-, 3.2.1.143, 3.2.2.-) | protein | 329 | 67% helix, 1% strand | H3BCW1 |
Ligands and binding sites
- RVK · Adenosine 5'-diphosphoric acid beta-[(3beta,4beta-dihydroxy-5beta-methoxytetrahydrofuran-2alpha-yl) methyl] estere · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1000 | 0.87 | 0.88 | 111 | RVK, MG |
| 2 | 107 | 0.42 | 0.77 | 24 | empty |
| 3 | 105 | 0.40 | 0.76 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 664 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7AQM · ADP-ribosylserine hydrolase ARH3 of Latimeria chalumnae in complex with… · 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 7AQM · PDBe 7AQM · UniProt H3BCW1
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