SMTL ID : 7wab.1

Crystal structure of the prolyl endoprotease, PEP, from Aspergillus niger

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-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: 23 residues within 4Å: Chain A: A.182, Q.183, N.184, D.241, F.242, V.243, T.244, G.245, Y.246, F.250, C.253, D.254, E.257, V.259, E.260, G.262, A.263, T.266, P.267, P.269, F.448, A.460, N.461 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.266 Hydrogen bonds: A:D.254, A:G.262, A:A.263

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

NAG-NAG.2: 6 residues within 4Å: Chain A: G.216, N.283, N.286, S.287, L.290, W.304 No protein-ligand interaction detected (PLIP)

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

NAG.3: 4 residues within 4Å: Chain A: Y.31, N.58, Q.67, Y.459 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.58, A:Q.67, A:Y.459, A:Y.459 NAG.4: 6 residues within 4Å: Chain A: E.221, D.310, N.313, S.315, S.316, P.317 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.310, A:N.313 Water bridges: A:N.313

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miyazono, K.I. et al., Crystal structure and substrate recognition mechanism of the prolyl endoprotease PEP from Aspergillus niger. Biochem.Biophys.Res.Commun. (2022)

Release Date

2022-01-12

Peptides

COMPASS (Complex proteins associated with Set1p) component shg1 family protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

COMPASS (Complex proteins associated with Set1p) component shg1 family protein