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Crystal structure of AP4A hydrolase complexed with AP4A (ATP) (AQ_158) from aquifex aeolicus VF5
Analyse Crystal structure of AP4A hydrolase complexed with AP4A (ATP) (AQ_158) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3I7V
- Type
- protein
- Length
- 268 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AP4A hydrolase
- UniProt
- O66548
- Ligands
- ATP, B4P
- Pockets
- 2 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | AP4A hydrolase | protein | 134 | 27% helix, 47% strand | O66548 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- B4P · Bis(adenosine)-5'-tetraphosphate · ligand · chains A, B
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 447 | 0.62 | 0.76 | 52 | ATP, B4P, EDO |
| 2 | 119 | 0.41 | 0.76 | 27 | ATP, EDO |
Interfaces
1 interface between chains.
- A–B · 462 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3I7V · Crystal structure of AP4A hydrolase complexed with AP4A (ATP) (aq_158) from Aquifex… · 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 O66548
- Elsewhere: RCSB PDB 3I7V · PDBe 3I7V · UniProt O66548
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