MolNFT v1 · #34759 · protein

Crystal structure of aminopeptidase N from escherichia COLI

2DQ6: “Crystal structure of aminopeptidase N from escherichia COLI”. X-ray diffraction, 2 ligands (ZN, SO4), 12 pockets (best druggability 0.80). MolNFT v1 #34759 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2DQ6
Type: protein
Length: 865 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: ZN, SO4
Pockets: 12 · best druggability 0.80

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	865	45% helix, 22% strand	P04825

Ligands and binding sites

ZN · Zinc ion · metal · chains A
SO4 · Sulfate ion · ion · 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, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	420	0.80	0.88	64	SO4
2	514	0.74	0.82	58	empty
3	242	0.71	0.86	36	empty
4	193	0.68	0.86	31	empty
5	514	0.67	0.78	56	empty

Compared structures

2DQ6 · Crystal Structure of Aminopeptidase N from Escherichia coli · 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 2DQ6 · PDBe 2DQ6 · UniProt P04825

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