Research workbench
Structure of epepn E298A mutant in complex with puromycin
Analyse Structure of epepn E298A mutant in complex with puromycin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YO1
- Type
- protein
- Length
- 866 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminopeptidase N
- EC
- 3.4.11.2
- UniProt
- P04825
- Ligands
- PUY, ZN, NA
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminopeptidase N (EC 3.4.11.2) | protein | 866 | 44% helix, 22% strand | P04825 |
Ligands and binding sites
- PUY · Puromycin · ligand · 2 copies · chains A
- ZN · Zinc ion · metal · chains A
- NA · Sodium ion · metal · chains A
- GOL · Glycerol · additive · 12 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 401 | 0.78 | 0.87 | 63 | PUY, GOL |
| 2 | 337 | 0.75 | 0.86 | 52 | GOL |
| 3 | 410 | 0.71 | 0.82 | 45 | GOL |
| 4 | 650 | 0.70 | 0.78 | 62 | GOL |
| 5 | 51 | 0.54 | 0.89 | 18 | empty |
Compared structures
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 P04825
- Elsewhere: RCSB PDB 5YO1 · PDBe 5YO1 · UniProt P04825
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