SMTL ID : 6ydx.1 (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

3 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: 6 residues within 4Å: Chain A: H.59, P.60, N.61, T.63, D.199, L.220 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.541, S.543, T.561, E.562 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.727, K.757, S.760 No protein-ligand interaction detected (PLIP)

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: 3 residues within 4Å: Chain A: N.455, H.456, D.468 No protein-ligand interaction detected (PLIP)

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.5: 19 residues within 4Å: Chain A: E.172, G.305, A.306, E.308, K.337, I.338, H.341, E.342, H.345, E.364, E.371, Y.372, F.421, D.422, S.423, Y.426, F.427, Y.838 Ligands: ZN.6 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.338, A:Y.426, A:Y.426, A:F.427 Hydrogen bonds: A:E.172, A:G.305, A:H.341, A:Y.372 pi-Stacking: A:H.341, A:Y.838

1 x ZN: ZINC ION(Non-covalent)

ZN.6: 6 residues within 4Å: Chain A: E.308, H.341, H.345, E.364, Y.426 Ligands: ONN.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.345, A:E.364

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

NAG.7: 2 residues within 4Å: Chain A: N.92 Ligands: NAG.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.92, A:N.92 NAG.8: 4 residues within 4Å: Chain A: Q.76, G.131, H.132, N.133 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.76, A:N.133 NAG.9: 3 residues within 4Å: Chain A: N.245, S.247 Ligands: PG4.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.245 NAG.10: 2 residues within 4Å: Chain A: Q.677, N.711 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.677, A:N.711 NAG.11: 6 residues within 4Å: Chain A: G.90, H.91, N.92, S.141, N.143 Ligands: NAG.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.141

1 x SIN: SUCCINIC ACID(Non-covalent)

SIN.12: 5 residues within 4Å: Chain A: K.437, T.438, I.571, N.572, N.574 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.572, A:N.574 Salt bridges: A:K.437

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

EDO.13: 3 residues within 4Å: Chain A: T.89, A.115, G.118 No protein-ligand interaction detected (PLIP) EDO.14: 1 residues within 4Å: Chain A: K.896 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.896, A:K.896

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.16: 1 residues within 4Å: Ligands: NAG.9 No protein-ligand interaction detected (PLIP)

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.17: 2 residues within 4Å: Chain A: R.667, T.904 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.667

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
A

Leucyl-cystinyl aminopeptidase

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