Research workbench

Crystal structure of E. COLI aminopeptidase N in complex with lysine

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

PDB: 3B2X
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: LYS, NA, ZN
Pockets: 12 · best druggability 0.78

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

LYS · Lysine · ligand · chains A
NA · Sodium ion · metal · 2 copies · chains A
ZN · Zinc ion · metal · chains A
GOL · Glycerol · additive · 9 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

12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	298	0.78	0.90	44	LYS, MLI, GOL
2	401	0.76	0.86	57	MLI
3	494	0.73	0.82	57	GOL
4	211	0.72	0.88	32	empty
5	622	0.69	0.78	60	empty

Compared structures

3B2X · Crystal Structure of E. coli Aminopeptidase N in complex with Lysine · 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 3B2X · PDBe 3B2X · UniProt P04825

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.