Research workbench
Crystal structure of E.COLI aminopeptidase N in complex with puromycin
Analyse Crystal structure of E.COLI aminopeptidase N 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
- 5YQB
- 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
- 0A1, GMC, ZN
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminopeptidase N (EC 3.4.11.2) | protein | 866 | 45% helix, 22% strand | P04825 |
Ligands and binding sites
- 0A1 · O-methyl-L-tyrosine · ligand · chains A
- GMC · (2R,3R,4S,5S)-4-amino-2-[6-(dimethylamino)-9H-purin-9-yl]-5-(hydroxymethyl)tetrahydro-3-furanol · ligand · chains A
- ZN · Zinc ion · metal · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 785 | 0.82 | 0.85 | 99 | 0A1, GMC |
| 2 | 660 | 0.79 | 0.84 | 63 | empty |
| 3 | 263 | 0.72 | 0.86 | 41 | empty |
| 4 | 555 | 0.65 | 0.76 | 63 | empty |
| 5 | 136 | 0.46 | 0.78 | 26 | 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 5YQB · PDBe 5YQB · UniProt P04825
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