SMTL ID : 6xut.1

Crystallographic structure of oligosaccharide dehydrogenase from Pycnoporus cinnabarinus, ligand-free form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- BMA- BMA: beta-D-mannopyranose-(1-3)-[beta-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-BMA-BMA.1: 7 residues within 4Å: Chain A: V.307, A.385, A.386, N.439, T.441, N.454, N.456 No protein-ligand interaction detected (PLIP)

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: 3 residues within 4Å: Chain A: N.38, L.41, Q.591 No protein-ligand interaction detected (PLIP)

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.3: 39 residues within 4Å: Chain A: V.22, G.23, G.24, G.25, L.26, T.27, I.46, E.47, A.48, Y.64, F.68, W.74, H.85, G.87, K.88, T.89, G.91, G.92, S.93, S.94, N.97, G.98, A.99, A.100, H.245, M.246, A.247, A.287, A.288, G.289, Q.292, A.527, H.528, D.560, A.561, H.571, L.572, S.573, L.576 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:Y.64, A:F.68, A:A.527 Hydrogen bonds: A:L.26, A:T.27, A:A.48, A:G.87, A:T.89, A:S.93, A:S.93, A:N.97, A:G.98, A:A.99, A:A.100, A:A.100, A:A.247, A:A.247, A:A.561, A:L.572, A:S.573 Water bridges: A:G.25, A:G.28, A:S.93, A:S.93, A:A.290, A:Q.292, A:S.574 pi-Stacking: A:H.528

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

NAG.4: 1 residues within 4Å: Chain A: N.188 No protein-ligand interaction detected (PLIP)

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

SO4.5: 4 residues within 4Å: Chain A: G.124, N.126, N.128, N.129 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.126, A:N.128, A:N.129 SO4.6: 4 residues within 4Å: Chain A: I.155, H.194, Y.195, K.196 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.196 Water bridges: A:D.197 Salt bridges: A:K.196 SO4.7: 3 residues within 4Å: Chain A: G.518, N.519, S.520 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.519 Water bridges: A:S.520, A:S.520 SO4.8: 3 residues within 4Å: Chain A: E.172, G.345, H.346 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.346 Water bridges: A:H.346 Salt bridges: A:H.346 SO4.9: 3 residues within 4Å: Chain A: N.144, D.145, Q.146 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.145, A:Q.146 Water bridges: A:N.144, A:N.144, A:D.145, A:D.145, A:Q.146 SO4.10: 3 residues within 4Å: Chain A: G.254, T.255, N.256 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.255, A:N.256, A:N.256 SO4.11: 3 residues within 4Å: Chain A: R.472, T.506, D.507 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.507, A:D.507, A:D.507 Salt bridges: A:R.472 SO4.12: 2 residues within 4Å: Chain A: T.272, G.273 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.273, A:G.273

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cerutti, G. et al., Crystal structure and functional characterization of an oligosaccharide dehydrogenase from Pycnoporus cinnabarinus provides insights into fungal breakdown of lignocellulose. Biotechnol Biofuels (2021)

Release Date

2021-02-03

Peptides

Oligosaccharide dehydrogenase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Oligosaccharide dehydrogenase

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