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

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.53 Å

Oligo State

monomer

Ligands

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.1: 7 residues within 4Å: Chain A: H.28, P.29, N.30, T.32, D.168, E.169, L.189 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.169, A:T.32

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.2: 4 residues within 4Å: Chain A: L.21, Q.45, G.100, N.102 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 3 residues within 4Å: Chain A: N.565, Y.567, N.606 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 6 residues within 4Å: Chain A: 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:E.441

4 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: 3 residues within 4Å: Chain A: N.214, L.215, S.216 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: N.510, S.512, T.530, E.531 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.530 NAG-NAG.8: 1 residues within 4Å: Chain A: N.61 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain A: Q.650, Q.651, Q.652, N.680 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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.5: 3 residues within 4Å: Chain A: E.128, N.696, S.729 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.128 NAG-NAG-BMA-MAN-MAN.7: 5 residues within 4Å: Chain A: N.220, Q.251, I.256, Q.257, H.423 No protein-ligand interaction detected (PLIP)

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

NAG.11: 3 residues within 4Å: Chain A: D.292, S.293, N.294 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.292 NAG.12: 2 residues within 4Å: Chain A: N.528, T.530 No protein-ligand interaction detected (PLIP) NAG.13: 2 residues within 4Å: Chain A: G.59, N.112 No protein-ligand interaction detected (PLIP) NAG.14: 2 residues within 4Å: Chain A: N.371, K.460 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.460

1 x ZN: ZINC ION(Non-covalent)

ZN.15: 5 residues within 4Å: Chain A: H.310, H.314, E.333, Y.395 Ligands: 7O2.16 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)

7O2.16: 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.15 15 PLIP interactions: 15 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, A:F.396, A:Y.807 Hydrogen bonds: A:E.141, A:G.274, A:A.275, A:Y.395 pi-Stacking: A:Y.395, A:Y.807

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

BR.17: 3 residues within 4Å: Chain A: T.407, S.503, V.517 Ligand excluded by PLIP BR.18: 4 residues within 4Å: Chain A: Q.650, G.679, N.680, C.681 Ligand excluded by PLIP BR.19: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP BR.20: 1 residues within 4Å: Chain A: S.26 Ligand excluded by PLIP BR.21: 1 residues within 4Å: Chain A: K.757 Ligand excluded by PLIP BR.22: 1 residues within 4Å: Chain A: W.754 Ligand excluded by PLIP BR.23: 1 residues within 4Å: Chain A: K.366 Ligand excluded by PLIP BR.24: 5 residues within 4Å: Chain A: G.629, M.631, D.632, P.880, A.881 Ligand excluded by PLIP BR.25: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP BR.26: 2 residues within 4Å: Chain A: I.12, R.146 Ligand excluded by PLIP BR.27: 4 residues within 4Å: Chain A: W.325, S.379, V.380, Q.381 Ligand excluded by PLIP BR.28: 1 residues within 4Å: Chain A: R.872 Ligand excluded by PLIP BR.29: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP BR.30: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP BR.31: 1 residues within 4Å: Chain A: Y.118 Ligand excluded by PLIP

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
A

Leucyl-cystinyl aminopeptidase

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