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Crystal structure of E. COLI aminopeptidase N in complex with L- leucine

Analyse Crystal structure of E. COLI aminopeptidase N in complex with L- leucine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4XO3
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: LEU, NA, ZN
Pockets: 10 · 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	866	44% helix, 22% strand	P04825

Ligands and binding sites

LEU · Leucine · ligand · chains A
NA · Sodium ion · metal · 11 copies · chains A
ZN · Zinc ion · metal · chains A
MLI · Malonate ion · additive · 3 copies · 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, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	621	0.83	0.88	70	LEU, GOL, MLI
2	457	0.78	0.86	54	MLI
3	291	0.73	0.86	38	NA
4	522	0.65	0.77	55	NA
5	67	0.58	0.89	20	empty

Compared structures

4XO3 · Crystal Structure of E. coli Aminopeptidase N in complex with L-Leucine · 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 4XO3 · PDBe 4XO3 · UniProt P04825

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