Research workbench
Structure of xac nucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE in complex with AMP
Analyse Structure of xac nucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GSU
- Type
- protein
- Length
- 764 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphodiesterase-nucleotide pyrophosphatase
- EC
- 3.6.1.9
- UniProt
- Q8PIS1
- Ligands
- AMP, ZN
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phosphodiesterase-nucleotide pyrophosphatase (EC 3.6.1.9) | protein | 382 | 35% helix, 21% strand | Q8PIS1 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- ZN · Zinc 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 947 | 0.81 | 0.83 | 108 | empty |
| 2 | 461 | 0.66 | 0.78 | 43 | AMP |
| 3 | 457 | 0.64 | 0.77 | 43 | AMP |
Interfaces
1 interface between chains.
- A–B · 682 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2GSU · Structure of Xac Nucleotide Pyrophosphatase/Phosphodiesterase in Complex with AMP · 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 Q8PIS1
- Elsewhere: RCSB PDB 2GSU · PDBe 2GSU · UniProt Q8PIS1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.