Research workbench
Crystal structure of E.coli aminopeptidase N in complex with O-Methyl-L-tyrosine
Analyse Crystal structure of E.coli aminopeptidase N in complex with O-Methyl-L-tyrosine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YQ1
- Type
- protein
- Length
- 866 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.58
- Source
- Escherichia coli (strain K12)
- Molecule
- Aminopeptidase N
- EC
- 3.4.11.2
- UniProt
- P04825
- Ligands
- 0A1, ZN
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · resolution 1.58 · 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
- ZN · Zinc ion · metal · chains A
- GOL · Glycerol · additive · 6 copies · chains A
- MLI · Malonate ion · additive · 3 copies · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1005 | 0.86 | 0.87 | 127 | 0A1, MLI, GOL |
| 2 | 285 | 0.72 | 0.85 | 36 | GOL |
| 3 | 543 | 0.67 | 0.78 | 60 | empty |
| 4 | 126 | 0.47 | 0.78 | 26 | empty |
| 5 | 93 | 0.42 | 0.78 | 17 | empty |
Compared structures
- 5YQ1 · Crystal structure of E.COLI aminopeptidase N in complex with O-methyl- L-tyrosine · the same entry in another collection · chain A against A, TM-score 1.00
- P04825 · AlphaFold monomer V2.0 prediction for aminopeptidase N (P04825) · a predicted model of the same protein · 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 P04825
- Elsewhere: RCSB PDB 5YQ1 · PDBe 5YQ1 · UniProt P04825
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