MolNFT v1 · #151223 · protein
ADP-ribosylserine hydrolase ARH3 of latimeria chalumnae in complex with ADP-hpd
6HH3 · ADP-ribosylhydrolase like 2: “ADP-ribosylserine hydrolase ARH3 of latimeria chalumnae in complex with ADP-hpd”. X-ray diffraction, 2 ligands (A1R, MG), 5 pockets (best druggability 0.87). MolNFT v1 #151223 on GenesisL1: 3D…
- PDB
- 6HH3
- Type
- protein
- Length
- 657 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosylhydrolase like 2
- UniProt
- H3BCW1
- Ligands
- A1R, MG
- Pockets
- 5 · 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 | protein | 329 | 67% helix, 1% strand | H3BCW1 |
| B | ADP-ribosylhydrolase like 2 | protein | 328 | 67% helix, 1% strand | H3BCW1 |
Ligands and binding sites
- A1R · 5'-O-[(S)-{[(S)-{[(2R,3R,4S)-3,4-dihydroxypyrrolidin-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy) phosphoryl]adenosine · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1110 | 0.87 | 0.88 | 117 | A1R |
| 2 | 79 | 0.43 | 0.80 | 22 | empty |
| 3 | 78 | 0.42 | 0.80 | 23 | empty |
| 4 | 82 | 0.40 | 0.78 | 23 | empty |
| 5 | 91 | 0.40 | 0.77 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 835 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6HH3 · ADP-ribosylserine hydrolase ARH3 of Latimeria chalumnae in complex with ADP-HPD · 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 6HH3 · PDBe 6HH3 · UniProt H3BCW1
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