SMTL ID : 8cgw.2 (1 other biounit)

Insulin-regulated aminopeptidase (IRAP) in complex with an allosteric benzopyran-based inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.03 Å

Oligo State

monomer

Ligands

2 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.1: 3 residues within 4Å: Chain A: N.696, K.726, S.729 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 7 residues within 4Å: Chain A: N.424, H.425, I.430, D.434, D.437, E.441, R.451 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.437, A:R.451, A:R.451

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.2: 4 residues within 4Å: Chain A: L.21, R.22, G.100, N.102 No protein-ligand interaction detected (PLIP)

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.3: 4 residues within 4Å: Chain A: N.30, S.33, D.168, L.189 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain A: I.649, Q.650, W.654, N.680, T.684 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.6: 4 residues within 4Å: Chain A: E.277, H.310, H.314, E.333 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.310, A:H.314, A:E.333, A:E.333

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

NAG.7: 2 residues within 4Å: Chain A: N.61 Ligands: NAG.8 No protein-ligand interaction detected (PLIP) NAG.8: 5 residues within 4Å: Chain A: G.59, S.110, A.111, N.112 Ligands: NAG.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.112 NAG.9: 4 residues within 4Å: Chain A: N.214, L.215, S.216, L.223 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.215 Hydrogen bonds: A:N.214, A:S.216, A:S.216 NAG.10: 3 residues within 4Å: Chain A: N.371, K.460, M.485 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.460 NAG.11: 3 residues within 4Å: Chain A: Y.567, N.606, H.607 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.606

2 x GLY: GLYCINE(Non-functional Binders)(Non-covalent)

GLY.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GLY.14: 2 residues within 4Å: Chain A: A.814, Y.818 2 PLIP interactions: 2 Ligand-Ligand interactions Hydrogen bonds: G.14, G.14

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

EDO.13: 1 residues within 4Å: Chain A: W.754 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.750

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mpakali, A. et al., Mechanisms of Allosteric Inhibition of Insulin-Regulated Aminopeptidase. J.Mol.Biol. (2024)

Release Date

2024-01-31

Peptides

Leucyl-cystinyl aminopeptidase, pregnancy serum form: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Leucyl-cystinyl aminopeptidase, pregnancy serum form

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