Research workbench
Crystal structure of E. COLI aminopeptidase N in complex with L- methionine
Analyse Crystal structure of E. COLI aminopeptidase N in complex with L- methionine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XO4
- Type
- protein
- Length
- 870 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
- MET, NA, ZN
- Pockets
- 11 · best druggability 0.83
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 | 870 | 44% helix, 22% strand | P04825 |
Ligands and binding sites
- MET · Methionine · ligand · 3 copies · chains A
- NA · Sodium ion · metal · 7 copies · chains A
- ZN · Zinc ion · metal · chains A
- GOL · Glycerol · additive · 2 copies · chains A
- MLI · Malonate ion · additive · 2 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 | 770 | 0.83 | 0.86 | 93 | MET, MLI |
| 2 | 264 | 0.72 | 0.86 | 37 | NA |
| 3 | 147 | 0.70 | 0.90 | 33 | empty |
| 4 | 514 | 0.64 | 0.76 | 58 | empty |
| 5 | 55 | 0.57 | 0.90 | 16 | empty |
Compared structures
- 4XO4 · Crystal Structure of E. coli Aminopeptidase N in complex with L-Methionine · 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 0.99
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 4XO4 · PDBe 4XO4 · UniProt P04825
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