SMTL ID : 5mj6.2 (1 other biounit)

Ligand-induced conformational change of Insulin-regulated aminopeptidase: insights on catalytic mechanism and active site plasticity.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.53 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.28, P.29, N.30, R.167, D.168, L.189 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.214, L.215, S.216, L.223 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain A: N.220, Q.257 No protein-ligand interaction detected (PLIP)

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.2: 7 residues within 4Å: Chain A: L.420, N.424, H.425, D.434, D.437, E.441, K.450 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.450, A:K.450 NAG-NAG-BMA.4: 3 residues within 4Å: Chain A: N.565, Y.567, N.606 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.567

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

6 x BR: BROMIDE ION(Non-covalent)(Non-functional Binders)

BR.7: 1 residues within 4Å: Chain A: W.754 Ligand excluded by PLIP BR.18: 4 residues within 4Å: Chain A: T.407, Y.408, S.503, V.517 Ligand excluded by PLIP BR.19: 1 residues within 4Å: Ligands: BR.22 Ligand excluded by PLIP BR.20: 1 residues within 4Å: Chain A: W.754 Ligand excluded by PLIP BR.21: 1 residues within 4Å: Chain A: H.423 Ligand excluded by PLIP BR.22: 3 residues within 4Å: Chain A: Y.354, K.572 Ligands: BR.19 Ligand excluded by PLIP

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

NAG.8: 2 residues within 4Å: Chain A: Q.650, N.680 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.650 Hydrogen bonds: A:N.680 NAG.9: 2 residues within 4Å: Chain A: N.61 Ligands: NAG.13 No protein-ligand interaction detected (PLIP) NAG.10: 4 residues within 4Å: Chain A: L.21, Q.45, G.100, N.102 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.45 NAG.11: 3 residues within 4Å: Chain A: N.510, S.512, E.531 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.510, A:S.512, A:S.512 NAG.12: 1 residues within 4Å: Chain A: N.528 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.528 NAG.13: 2 residues within 4Å: Chain A: N.112 Ligands: NAG.9 No protein-ligand interaction detected (PLIP) NAG.14: 2 residues within 4Å: Chain A: D.292, N.294 No protein-ligand interaction detected (PLIP) NAG.15: 2 residues within 4Å: Chain A: N.444, T.446 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.446, A:T.446

1 x ZN: ZINC ION(Non-covalent)

ZN.16: 5 residues within 4Å: Chain A: H.310, H.314, E.333, Y.395 Ligands: 7O2.17 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.310, A:H.314, A:E.333

1 x 7O2: [(2~{S})-2-[[(2~{S})-1-azanyl-1-oxidanylidene-3-phenyl-propan-2-yl]carbamoyl]-4,4-diphenyl-butyl]-[(1~{R})-1-azanyl-3-phenyl-propyl]phosphinic acid(Non-covalent)

7O2.17: 20 residues within 4Å: Chain A: E.141, A.273, G.274, A.275, M.276, E.277, L.303, I.307, H.310, E.311, H.314, E.333, T.337, E.340, F.390, D.391, Y.395, F.396, Y.807 Ligands: ZN.16 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:A.273, A:L.303, A:I.307, A:I.307, A:F.390, A:Y.395, A:F.396 Hydrogen bonds: A:E.141, A:G.274, A:A.275, A:Y.395, A:Y.395 pi-Stacking: A:Y.395, A:Y.807

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mpakali, A. et al., Ligand-Induced Conformational Change of Insulin-Regulated Aminopeptidase: Insights on Catalytic Mechanism and Active Site Plasticity. J. Med. Chem. (2017)

Release Date

2017-04-05

Peptides

Leucyl-cystinyl aminopeptidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Leucyl-cystinyl aminopeptidase

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