SMTL ID : 8cgw.1 (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

3 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: 6 residues within 4Å: Chain A: L.420, N.424, H.425, D.437, E.441, K.450 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.450, A:K.450, A:K.450 NAG-NAG-BMA.2: 2 residues within 4Å: Chain A: N.696, K.726 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 6 residues within 4Å: Chain A: H.28, P.29, N.30, D.168, Q.170, L.189 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.170

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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-MAN-MAN.3: 4 residues within 4Å: Chain A: S.524, V.526, I.527, N.528 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.4: 3 residues within 4Å: Chain A: N.214, L.215, S.216 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: G.59, S.110, N.112 No protein-ligand interaction detected (PLIP)

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.5: 5 residues within 4Å: Chain A: N.565, Y.567, N.606, H.607, M.662 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.8: 5 residues within 4Å: Chain A: E.277, H.310, E.311, 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

1 x UJX: ethyl 2-acetamido-7-hydroxy-4-(pyridin-3-yl)-4H-chromene-3-carboxylate(Non-covalent)

UJX.9: 11 residues within 4Å: Chain A: S.116, Y.117, Y.118, Q.139, E.141, P.142, A.273, G.274, A.275, E.387, F.390 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.118, A:Y.118, A:Y.118, A:P.142 Hydrogen bonds: A:E.387

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

NAG.10: 3 residues within 4Å: Chain A: Q.650, N.680 Ligands: GLY.18 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.650 NAG.11: 2 residues within 4Å: Chain A: N.61, I.62 No protein-ligand interaction detected (PLIP) NAG.12: 3 residues within 4Å: Chain A: Q.45, G.100, N.102 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.45, A:G.100 NAG.13: 3 residues within 4Å: Chain A: N.371, F.482, N.484 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.482 Hydrogen bonds: A:N.371 NAG.14: 1 residues within 4Å: Chain A: N.444 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.444 NAG.15: 2 residues within 4Å: Chain A: N.220, Q.257 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.257

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

PEG.16: 3 residues within 4Å: Chain A: H.560, K.563, I.564 No protein-ligand interaction detected (PLIP)

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

EDO.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x GLY: GLYCINE(Non-covalent)

GLY.18: 6 residues within 4Å: Chain A: I.649, W.654, N.680, C.681, T.684 Ligands: NAG.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.654, A:N.680, A:C.681, A:T.684 GLY.19: 2 residues within 4Å: Chain A: Y.341, K.406 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:Y.341, G.19, G.19 Salt bridges: A:K.406

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
A

Leucyl-cystinyl aminopeptidase, pregnancy serum form

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