SMTL ID : 5c1e.1

Crystal Structure of the Pectin Methylesterase from Aspergillus niger in Penultimately Deglycosylated Form (N-acetylglucosamine Stub at Asn84)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.1: 3 residues within 4Å: Chain A: N.56, Q.127, W.294 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.56 Water bridges: A:S.35

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: Y.150, W.170, G.172, K.283 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.150 Water bridges: A:E.173, A:D.201, A:D.201, A:N.202 Salt bridges: A:K.283 SO4.3: 3 residues within 4Å: Chain A: W.223, R.224 Ligands: GOL.8 4 PLIP interactions: 4 interactions with chain A Water bridges: A:W.223, A:R.224, A:R.224 Salt bridges: A:R.224 SO4.4: 4 residues within 4Å: Chain A: R.189, D.194, S.195, R.228 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.228, A:R.228 Salt bridges: A:R.228 SO4.5: 2 residues within 4Å: Chain A: E.190, R.224 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.224 SO4.6: 3 residues within 4Å: Chain A: T.191, S.192, S.193 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.192, A:S.193, A:S.193

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

CL.7: 2 residues within 4Å: Chain A: N.124, K.145 Ligand excluded by PLIP

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 7 residues within 4Å: Chain A: Q.117, D.140, D.161, F.164, W.223, M.248 Ligands: SO4.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.117, A:D.140, A:D.161 GOL.9: 3 residues within 4Å: Chain A: S.87, D.89, K.90 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.89 Water bridges: A:S.87, A:D.89, A:D.89, A:D.89, A:D.89, A:K.145 GOL.10: 4 residues within 4Å: Chain A: T.284, E.289, W.291, G.292 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.284, A:G.292 GOL.11: 2 residues within 4Å: Chain A: P.7, S.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.8 Water bridges: A:E.1 GOL.13: 3 residues within 4Å: Chain A: S.262, G.263, A.264 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.263 Water bridges: A:N.261, A:S.266

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.12: 2 residues within 4Å: Chain A: R.221, M.248 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.248 Salt bridges: A:R.221

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kent, L.M. et al., Structure and Properties of a Non-processive, Salt-requiring, and Acidophilic Pectin Methylesterase from Aspergillus niger Provide Insights into the Key Determinants of Processivity Control. J.Biol.Chem. (2016)

Release Date

2015-07-01

Peptides

Pectinesterase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Pectinesterase