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

Insulin regulated aminopeptidase (IRAP) in complex with an allosteric aryl sulfonamide inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.62 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-6)-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.1: 8 residues within 4Å: Chain A: H.28, P.29, N.30, T.32, K.132, Y.134, D.168, L.189 No protein-ligand interaction detected (PLIP)

4 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: G.100, N.102, K.199 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.199 NAG-NAG-BMA.3: 1 residues within 4Å: Chain A: N.112 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 4 residues within 4Å: Chain A: N.214, L.215, S.216, L.223 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 1 residues within 4Å: Chain A: N.61 No protein-ligand interaction detected (PLIP)

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.4: 6 residues within 4Å: Chain A: E.128, S.129, N.130, N.696, K.726, S.729 No protein-ligand interaction detected (PLIP)

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.6: 2 residues within 4Å: Chain A: N.371, N.484 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: Y.567, N.606, Q.651 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain A: N.220, Q.257 No protein-ligand interaction detected (PLIP)

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

NAG.10: 4 residues within 4Å: Chain A: N.424, H.425, D.434, E.441 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.434, A:D.437 NAG.11: 1 residues within 4Å: Chain A: N.510 No protein-ligand interaction detected (PLIP) NAG.12: 2 residues within 4Å: Chain A: N.294, S.700 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.700 NAG.13: 2 residues within 4Å: Chain A: Q.650, N.680 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.650

1 x MLT: D-MALATE(Non-covalent)

MLT.14: 11 residues within 4Å: Chain A: A.273, G.274, A.275, E.277, H.310, E.311, H.314, E.333, Y.395 Ligands: ZN.15, UKG.16 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.395 Hydrogen bonds: A:G.274, A:A.275, A:A.275, A:Y.395 Water bridges: A:E.141 Salt bridges: A:H.310, A:H.314

1 x ZN: ZINC ION(Non-covalent)

ZN.15: 5 residues within 4Å: Chain A: H.310, H.314, E.333, Y.395 Ligands: MLT.14 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.310, A:H.314, A:E.333

1 x UKG: 4-bromanyl-5-chloranyl-~{N}-[3-(1~{H}-1,2,3,4-tetrazol-5-yl)phenyl]thiophene-2-sulfonamide(Non-covalent)

UKG.16: 11 residues within 4Å: Chain A: G.274, K.306, I.307, H.310, E.340, Y.341, F.390, Y.395, F.396, Y.807 Ligands: MLT.14 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.307 Hydrogen bonds: A:G.274, A:K.306, A:E.340 Water bridges: A:Y.341 pi-Stacking: A:H.310, A:F.396, A:Y.807 Halogen bonds: A:F.390

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

EDO.17: 4 residues within 4Å: Chain A: S.114, S.116, Y.118, S.147 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.114, A:S.114, A:S.116

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

PEG.18: 2 residues within 4Å: Chain A: A.694, S.695 No protein-ligand interaction detected (PLIP)

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

Related Entries With Identical Sequence