Research workbench
Crystal structure of streptococcal asymmetric AP4A hydrolase and phosphodiesterase SPR1479/SAPH im complex with AMP
Analyse Crystal structure of streptococcal asymmetric AP4A hydrolase and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QFO
- Type
- protein
- Length
- 500 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein
- UniProt
- Q8DNX4
- Ligands
- AMP, FE, MN
- Pockets
- 3 · best druggability 0.54
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative uncharacterized protein | protein | 250 | 32% helix, 24% strand | Q8DNX4 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- FE · Fe (III) ion · metal · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 262 | 0.54 | 0.76 | 26 | AMP |
| 2 | 238 | 0.54 | 0.77 | 28 | AMP |
| 3 | 102 | 0.39 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1718 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 3QFO · Crystal structure of Streptococcal asymmetric Ap4A hydrolase and 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 Q8DNX4
- Elsewhere: RCSB PDB 3QFO · PDBe 3QFO · UniProt Q8DNX4
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