Research workbench
Crystal structure analysis of xac nucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE
Analyse Crystal structure analysis of xac nucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7N1S
- Type
- protein
- Length
- 765 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphodiesterase-nucleotide pyrophosphatase
- UniProt
- A0A0U5FM15
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphodiesterase-nucleotide pyrophosphatase | protein | 383 | 34% helix, 22% strand | A0A0U5FM15 |
| B | Phosphodiesterase-nucleotide pyrophosphatase | protein | 382 | 34% helix, 23% strand | A0A0U5FM15 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 2 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 | 945 | 0.83 | 0.84 | 105 | PG4 |
| 2 | 517 | 0.66 | 0.77 | 54 | empty |
| 3 | 434 | 0.64 | 0.77 | 43 | empty |
Interfaces
1 interface between chains.
- A–B · 686 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7N1S · Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phosphodiesterase · 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 A0A0U5FM15
- Elsewhere: RCSB PDB 7N1S · PDBe 7N1S · UniProt A0A0U5FM15
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