SMTL ID : 6ydx.2 (1 other biounit)

Insulin-regulated aminopeptidase complexed with a macrocyclic peptidic inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

monomer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain A: N.245, L.246, S.247 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.541, S.543, T.561 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.561

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.2: 6 residues within 4Å: Chain A: H.59, P.60, N.61, T.63, D.199, L.220 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.63

1 x ONN: 2-[2-[[[(4~{R},8~{S},11~{S})-11-azanyl-8-[(4-hydroxyphenyl)methyl]-6,10-bis(oxidanylidene)-1,2-dithia-5,9-diazacyclotridec-4-yl]carbonylamino]methyl]phenyl]ethanoic acid(Non-covalent)

ONN.4: 20 residues within 4Å: Chain A: E.172, E.303, G.305, A.306, M.307, E.308, R.316, K.337, I.338, H.341, E.342, H.345, E.364, E.371, F.421, Y.426, S.802, R.806, Y.838 Ligands: ZN.5 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.338, A:Y.838 Hydrogen bonds: A:G.305, A:K.337, A:E.364, A:S.802, A:S.802 Salt bridges: A:R.316, A:R.806

1 x ZN: ZINC ION(Non-covalent)

ZN.5: 5 residues within 4Å: Chain A: H.341, H.345, E.364, Y.426 Ligands: ONN.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.341, A:H.345, A:E.364

5 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.6: 3 residues within 4Å: Chain A: L.451, N.455, H.456 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.455 NAG.7: 1 residues within 4Å: Chain A: N.133 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.133 NAG.8: 4 residues within 4Å: Chain A: G.90, H.91, N.92, N.143 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.92 NAG.9: 1 residues within 4Å: Chain A: N.727 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.727 NAG.10: 1 residues within 4Å: Chain A: N.161 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.161

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.11: 3 residues within 4Å: Chain A: M.208, S.226, E.227 No protein-ligand interaction detected (PLIP) EDO.12: 1 residues within 4Å: Chain A: R.540 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.540, A:R.540 EDO.13: 2 residues within 4Å: Chain A: K.437, T.438 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.437, A:K.437

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.14: 1 residues within 4Å: Chain A: Q.288 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.288

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mpakali, A. et al., Structural Basis of Inhibition of Insulin-Regulated Aminopeptidase by a Macrocyclic Peptidic Inhibitor. Acs Med.Chem.Lett. (2020)

Release Date

2020-07-22

Peptides

Leucyl-cystinyl aminopeptidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Leucyl-cystinyl aminopeptidase

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