Zinc in PDB 6ydx: Insulin-Regulated Aminopeptidase Complexed with A Macrocyclic Peptidic Inhibitor

All present enzymatic activity of Insulin-Regulated Aminopeptidase Complexed with A Macrocyclic Peptidic Inhibitor:
3.4.11.3;

The structure of Insulin-Regulated Aminopeptidase Complexed with A Macrocyclic Peptidic Inhibitor, PDB code: 6ydx was solved by A.Mpakali, E.Saridakis, P.Giastas, E.Stratikos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.96 / 3.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.419, 118.631, 141.389, 90.00, 102.77, 90.00
R / Rfree (%)	27.7 / 31.4

The binding sites of Zinc atom in the Insulin-Regulated Aminopeptidase Complexed with A Macrocyclic Peptidic Inhibitor (pdb code 6ydx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Insulin-Regulated Aminopeptidase Complexed with A Macrocyclic Peptidic Inhibitor, PDB code: 6ydx:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Insulin-Regulated Aminopeptidase Complexed with A Macrocyclic Peptidic Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Insulin-Regulated Aminopeptidase Complexed with A Macrocyclic Peptidic Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1102 b:49.3 occ:1.00 O33 A:ONN1101 2.1 39.7 0.4 OE1 A:GLU487 2.2 34.5 1.0 O33 A:ONN1101 2.2 39.8 0.6 NE2 A:HIS468 2.2 38.5 1.0 CE1 A:HIS464 2.5 34.5 1.0 N34 A:ONN1101 2.5 39.1 0.4 C31 A:ONN1101 2.6 39.8 0.4 C31 A:ONN1101 2.7 39.7 0.6 C32 A:ONN1101 3.0 39.3 0.4 CD2 A:HIS468 3.2 40.6 1.0 CE1 A:HIS468 3.2 40.8 1.0 ND1 A:HIS464 3.3 33.0 1.0 CD A:GLU487 3.3 35.2 1.0 N30 A:ONN1101 3.4 40.6 0.6 N34 A:ONN1101 3.4 39.8 0.6 C32 A:ONN1101 3.5 38.7 0.6 C1 A:ONN1101 3.5 41.4 0.6 NE2 A:HIS464 3.6 36.7 1.0 N30 A:ONN1101 3.7 40.4 0.4 CE2 A:TYR549 3.8 36.3 1.0 OE2 A:GLU487 3.8 41.0 1.0 OE1 A:GLU431 3.8 34.7 1.0 C9 A:ONN1101 3.9 40.2 0.6 OH A:TYR549 4.0 34.8 1.0 C1 A:ONN1101 4.1 41.3 0.4 ND1 A:HIS468 4.3 41.2 1.0 CG A:HIS468 4.3 39.4 1.0 C9 A:ONN1101 4.4 40.0 0.4 CZ A:TYR549 4.4 30.4 1.0 C35 A:ONN1101 4.5 38.1 0.4 CG A:GLU487 4.5 36.5 1.0 CG A:HIS464 4.6 35.5 1.0 C2 A:ONN1101 4.6 43.0 0.6 CB A:GLU487 4.6 38.2 1.0 CD2 A:HIS464 4.7 36.8 1.0 OE1 A:GLU465 4.7 39.7 1.0 CA A:GLU487 4.8 39.2 1.0 CB A:ALA490 4.8 32.0 1.0 CD2 A:TYR549 4.8 32.4 1.0 OE2 A:GLU465 4.8 33.9 1.0 C3 A:ONN1101 4.8 44.4 0.6 C35 A:ONN1101 4.9 38.3 0.6 C36 A:ONN1101 4.9 39.5 0.4 CD A:GLU431 5.0 37.1 1.0

Zinc binding site 2 out of 2 in the Insulin-Regulated Aminopeptidase Complexed with A Macrocyclic Peptidic Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Insulin-Regulated Aminopeptidase Complexed with A Macrocyclic Peptidic Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1102 b:35.2 occ:1.00 OE1 B:GLU487 2.2 33.8 1.0 NE2 B:HIS468 2.2 32.6 1.0 O33 B:ONN1101 2.2 37.0 0.6 NE2 B:HIS464 2.3 36.9 1.0 O33 B:ONN1101 2.5 45.9 0.5 CD2 B:HIS468 2.6 32.8 1.0 CD2 B:HIS464 3.2 36.3 1.0 CD B:GLU487 3.2 36.1 1.0 CE1 B:HIS464 3.3 37.8 1.0 C1 B:ONN1101 3.3 48.1 0.5 C31 B:ONN1101 3.4 48.1 0.5 C31 B:ONN1101 3.4 38.3 0.6 CE1 B:HIS468 3.5 34.0 1.0 OE2 B:GLU487 3.6 33.6 1.0 C1 B:ONN1101 3.7 38.2 0.6 CG B:HIS468 3.9 30.2 1.0 CE2 B:TYR549 4.0 40.1 1.0 N30 B:ONN1101 4.1 48.5 0.5 C9 B:ONN1101 4.2 51.5 0.5 N30 B:ONN1101 4.3 38.2 0.6 ND1 B:HIS468 4.3 30.6 1.0 C9 B:ONN1101 4.3 37.2 0.6 CG B:HIS464 4.3 33.3 1.0 C32 B:ONN1101 4.3 48.5 0.5 N34 B:ONN1101 4.4 47.5 0.5 ND1 B:HIS464 4.4 31.3 1.0 C32 B:ONN1101 4.4 39.0 0.6 CG B:GLU487 4.4 32.9 1.0 N34 B:ONN1101 4.4 39.2 0.6 OE2 B:GLU465 4.5 29.8 1.0 C2 B:ONN1101 4.5 49.5 0.5 OE2 B:GLU431 4.5 35.7 1.0 CA B:GLU487 4.5 31.8 1.0 CB B:GLU487 4.6 31.9 1.0 OH B:TYR549 4.6 40.3 1.0 CB B:ALA490 4.6 29.0 1.0 OE1 B:GLU465 4.7 36.3 1.0 C2 B:ONN1101 4.8 38.9 0.6 CZ B:TYR549 4.8 38.5 1.0 CD2 B:TYR549 4.8 35.2 1.0 CD B:GLU431 4.9 36.1 1.0 CD B:GLU465 5.0 35.1 1.0 C3 B:ONN1101 5.0 41.0 0.6

A.Mpakali, E.Saridakis, P.Giastas, Z.Maben, L.J.Stern, M.Larhed, M.Hallberg, E.Stratikos. Structural Basis of Inhibition of Insulin-Regulated Aminopeptidase By A Macrocyclic Peptidic Inhibitor. Acs Med.Chem.Lett. V. 11 1429 2020.
ISSN: ISSN 1948-5875
PubMed: 32676150
DOI: 10.1021/ACSMEDCHEMLETT.0C00172