SMTL ID : 8p0i.1 (1 other biounit)

Crystal structure of the open conformation of insulin-regulated aminopeptidase in complex with a small-MW inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.50 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: 5 residues within 4Å: Chain A: H.28, P.29, N.30, D.168, Q.170 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.168, A:Q.170 NAG-NAG-BMA.3: 5 residues within 4Å: Chain A: N.424, H.425, D.434, D.437, E.441 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.437 NAG-NAG-BMA.5: 2 residues within 4Å: Chain A: Y.567, N.606 No protein-ligand interaction detected (PLIP)

2 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: 2 residues within 4Å: Chain A: N.214, S.216 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.4: 2 residues within 4Å: Chain A: V.526, N.528 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.6: 2 residues within 4Å: Chain A: S.110, N.112 No protein-ligand interaction detected (PLIP)

7 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose

NAG.7: 1 residues within 4Å: Chain A: N.61 No protein-ligand interaction detected (PLIP) NAG.8: 1 residues within 4Å: Chain A: N.680 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.680 NAG.9: 2 residues within 4Å: Chain A: N.696, K.726 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.696, A:K.726 NAG.10: 3 residues within 4Å: Chain A: V.219, N.220, E.248 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.219 NAG.11: 3 residues within 4Å: Chain A: N.371, H.374, K.460 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.374, A:K.460 NAG.12: 2 residues within 4Å: Chain A: D.292, N.294 No protein-ligand interaction detected (PLIP) NAG.15: 4 residues within 4Å: Chain A: L.21, Q.45, G.100, N.102 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.21 Hydrogen bonds: A:Q.45

1 x WC3: 2-[2-(3,5-dimethylpyrazol-1-yl)-6-(4-methoxyphenyl)pyrimidin-4-yl]oxy-N-methyl-N-[(2-methylpyridin-3-yl)methyl]ethanamide

WC3.13: 18 residues within 4Å: Chain A: Y.118, E.141, P.142, Y.203, A.275, E.277, I.307, H.310, E.311, H.314, L.329, N.332, E.333, E.340, E.387, F.390, Y.395 Ligands: ZN.14 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.118, A:A.275, A:I.307, A:L.329, A:N.332, A:F.390 Hydrogen bonds: A:E.141

1 x ZN: ZINC ION

ZN.14: 6 residues within 4Å: Chain A: E.277, H.310, E.311, H.314, E.333 Ligands: WC3.13 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.310, A:H.314, A:E.333, A:E.333

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mpakali, A. et al., Stabilization of the open conformation omicron f insulin-regulated aminopeptidase by a novel substrate-selective small-molecule inhibitor. Protein Sci. (2024)

Release Date

2024-09-04

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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