SMTL ID : 4yn3.3 (2 other biounits)

Crystal structure of Cucumisin complex with pro-peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- FUC: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-FUC.1: 14 residues within 4Å: Chain A: P.200, K.223, N.311, T.312, R.313, D.314, I.354, N.356, V.361, R.368, R.454, F.455, N.456, P.457 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.312, A:R.313, A:F.455, A:N.456, A:N.311, A:R.313 Water bridges: A:D.327, A:R.368, A:F.455 Hydrophobic interactions: A:F.455

1 x NAG- FUC- NAG: alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-FUC-NAG.2: 4 residues within 4Å: Chain A: N.542, T.544, R.582, S.584 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.584

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 2 residues within 4Å: Chain A: P.79, I.80 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: E.57, T.58, S.59 Ligand excluded by PLIP

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

PEG.5: 5 residues within 4Å: Chain A: R.3, D.221, T.353, I.354, L.355 No protein-ligand interaction detected (PLIP) PEG.6: 4 residues within 4Å: Chain A: N.197, Y.315, F.365, S.412 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.412 Water bridges: A:N.197, A:N.197, A:N.197, B:E.94 PEG.7: 4 residues within 4Å: Chain A: Q.19, S.22, G.44, L.126 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.19 PEG.8: 5 residues within 4Å: Chain A: P.360, S.449, P.450, M.451, H.467 5 PLIP interactions: 5 interactions with chain A Water bridges: A:F.7, A:P.360, A:P.360, A:N.452, A:H.467

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 5 residues within 4Å: Chain A: D.158, G.188, K.429, P.433, W.435 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.158, A:D.158, A:W.435

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sotokawauchi, A. et al., Structural basis of cucumisin protease activity regulation by its propeptide. J. Biochem. (2017)

Release Date

2016-03-09

Peptides

Cucumisin: A
Cucumisin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cucumisin

Cucumisin

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