Research workbench
ADP ribose pyrophosphatase from thermus thermophilus HB8 in esm-state at reaction time of 3 min
Analyse ADP ribose pyrophosphatase from thermus thermophilus HB8 in esm-state at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3X0M
- Type
- protein
- Length
- 156 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribose pyrophosphatase
- EC
- 3.6.1.13
- UniProt
- Q5SKW5
- Ligands
- AR6, MN, SO4
- Pockets
- 1 · best druggability 0.45
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ADP-ribose pyrophosphatase (EC 3.6.1.13) | protein | 156 | 22% helix, 43% strand | Q5SKW5 |
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 · chains A
- MN · Manganese (II) ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 190 | 0.45 | 0.74 | 22 | MN |
Compared structures
- 3X0M · ADP ribose pyrophosphatase from Thermus thermophilus HB8 in ESM-state at reaction time of… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q5SKW5
- Elsewhere: RCSB PDB 3X0M · PDBe 3X0M · UniProt Q5SKW5
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