SMTL ID : 8b57.1

Structure of prolyl endoprotease from Aspergillus niger CBS 109712

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.42 Å

Oligo State

monomer

Ligands

2 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: 5 residues within 4Å: Chain A: E.31, Y.32, N.59, Q.68, Y.460 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.314, S.316, S.317, P.318 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN-MAN-MAN-MAN-MAN.2: 26 residues within 4Å: Chain A: A.183, Q.184, N.185, D.242, F.243, A.244, T.245, G.246, Y.247, F.251, C.254, D.255, E.258, V.260, E.261, A.262, G.263, A.264, A.265, T.267, P.268, P.270, F.449, A.461, N.462 Ligands: GOL.9 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.267 Hydrogen bonds: A:D.255, A:G.263, A:A.264

1 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.3: 5 residues within 4Å: Chain A: G.217, N.287, S.288, L.291, W.305 No protein-ligand interaction detected (PLIP)

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

NAG.5: 1 residues within 4Å: Chain A: N.121 No protein-ligand interaction detected (PLIP) NAG.6: 4 residues within 4Å: Chain A: D.198, K.199, K.202, N.203 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.198, A:K.202 Hydrogen bonds: A:N.203 NAG.7: 1 residues within 4Å: Chain A: N.405 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.405

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 1 residues within 4Å: Chain A: S.297 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.297, A:S.297 GOL.9: 4 residues within 4Å: Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.2, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.2, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.2, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.2 No protein-ligand interaction detected (PLIP)

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

PEG.10: 4 residues within 4Å: Chain A: G.52, Y.53, T.61, Y.455 No protein-ligand interaction detected (PLIP)

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.11: 8 residues within 4Å: Chain A: E.47, S.138, Y.139, Y.236, Q.239, D.240, Q.346, W.419 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.139

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.12: 9 residues within 4Å: Chain A: E.47, Y.53, Y.56, D.240, D.242, H.450, C.451, L.454, Y.455 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pijning, T. et al., Structural and time-resolved mechanistic investigations of protein hydrolysis by the acidic proline-specific endoprotease from Aspergillus niger. Protein Sci. (2024)

Release Date

2023-12-20

Peptides

Prolyl Endoprotease from Aspergillus niger CBS 109712: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Prolyl Endoprotease from Aspergillus niger CBS 109712

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