SMTL ID : 5l6g.1

Xylooligosaccharide oxidase from Myceliophthora thermophila C1 in complex with Xylose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.79 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: A.68, R.114, M.115, N.117, Q.130 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 6 residues within 4Å: Chain A: L.190, N.192, S.194, N.203, Q.479, L.480 No protein-ligand interaction detected (PLIP)

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.3: 34 residues within 4Å: Chain A: F.53, P.89, K.90, S.91, G.92, G.93, H.94, S.95, Y.96, F.99, G.100, L.112, P.131, G.153, T.154, C.155, V.158, G.159, G.161, G.162, H.163, L.165, H.166, G.168, F.169, G.214, S.215, G.218, I.219, V.220, Y.448, N.450, Y.451 Ligands: XYP.7 32 PLIP interactions: 32 interactions with chain A Hydrophobic interactions: A:F.53, A:H.94, A:Y.96, A:V.158 Hydrogen bonds: A:S.91, A:G.92, A:G.93, A:H.94, A:S.95, A:G.100, A:T.154, A:G.159, A:G.159, A:G.161, A:G.162, A:H.163, A:G.168, A:F.169, A:F.169, A:V.220, A:V.220, A:Y.448, A:N.450, A:N.450 Water bridges: A:N.88, A:N.88, A:G.93, A:Y.96, A:S.215, A:Y.451, A:Y.488 pi-Stacking: A:H.163

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

NAG.4: 5 residues within 4Å: Chain A: P.232, N.233, E.313, H.314, D.315 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.313 Water bridges: A:Y.143, A:P.232 NAG.5: 3 residues within 4Å: Chain A: N.245, S.247, N.248 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.245, A:S.247, A:S.247, A:N.248 Water bridges: A:P.242, A:T.244, A:T.244, A:S.247 NAG.6: 2 residues within 4Å: Chain A: N.289, S.291 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.289, A:S.291, A:S.291

3 x XYP: beta-D-xylopyranose(Non-covalent)

XYP.7: 10 residues within 4Å: Chain A: Y.96, T.154, C.155, R.272, Y.325, Y.376, I.378, E.412, Y.451 Ligands: FAD.3 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Y.96, A:T.154, A:T.154, A:R.272, A:R.272, A:Y.376 Water bridges: A:F.169, A:R.272, A:D.380 XYP.8: 6 residues within 4Å: Chain A: R.56, L.57, Y.343, F.426, P.454, G.455 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.56 XYP.9: 2 residues within 4Å: Chain A: H.176, D.181 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.181

1 x XYS: alpha-D-xylopyranose(Non-covalent)

XYS.10: 4 residues within 4Å: Chain A: A.277, F.278, N.369, K.370 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.277, A:A.277, A:K.370, A:K.370 Water bridges: A:N.369, A:N.369

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ferrari, A.R. et al., Discovery of a Xylooligosaccharide Oxidase from Myceliophthora thermophila C1. J.Biol.Chem. (2016)

Release Date

2016-09-21

Peptides

FAD linked oxidase-like protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

FAD linked oxidase-like protein

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