SMTL ID : 6xuu.1

Crystallographic structure of oligosaccharide dehydrogenase from Pycnoporus cinnabarinus, glucose-bound form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.57 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: 3 residues within 4Å: Chain A: N.38, S.40, L.41 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 8 residues within 4Å: Chain A: V.307, K.324, A.385, A.386, N.439, T.441, N.454, N.456 No protein-ligand interaction detected (PLIP)

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

FAD.3: 41 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 Ligands: BGC.7, GLC.12 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:F.68, A:A.527 Hydrogen bonds: A:L.26, A:T.27, A:A.48, A:G.87, A:S.93, A:S.93, A:S.94, 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:H.571, A:L.572, A:S.573 Water bridges: A:G.25, A:G.28, A:S.93, A:S.93, A:A.290, A:A.290, A:Q.292, A:S.574 pi-Cation interactions: A:H.571

8 x BGC: beta-D-glucopyranose(Non-covalent)

BGC.4: 9 residues within 4Å: Chain A: A.33, R.34, E.37, P.164, A.227, Y.228, P.231, V.232, R.236 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.37, A:Y.228, A:R.236 Water bridges: A:A.33, A:A.227, A:R.236 Salt bridges: A:R.34 BGC.5: 8 residues within 4Å: Chain A: S.141, A.142, N.144, Q.147, T.168, F.169, D.171, W.215 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:A.142, A:N.144, A:Q.147, A:T.168, A:T.168 Water bridges: A:D.171, A:D.171 BGC.6: 11 residues within 4Å: Chain A: Q.331, N.332, A.333, F.421, N.519, S.520, A.521, G.522, A.524 Ligands: BGC.8, BGC.11 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.331, A:N.332, A:A.333, A:N.519 Water bridges: A:W.513, A:A.521 BGC.7: 11 residues within 4Å: Chain A: Y.64, G.98, A.100, Q.331, F.416, V.526, H.528, H.571 Ligands: FAD.3, BGC.8, GLC.12 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.64, A:G.98, A:Q.331, A:V.526 Salt bridges: A:H.528, A:H.571 BGC.8: 6 residues within 4Å: Chain A: Y.64, D.418 Ligands: BGC.6, BGC.7, BGC.11, GLC.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.418 Water bridges: A:Y.64 BGC.9: 3 residues within 4Å: Chain A: N.106, D.110, W.127 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.110 Water bridges: A:D.110, A:W.127, A:N.128 BGC.10: 5 residues within 4Å: Chain A: V.189, T.190, Q.359, G.362, K.476 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.190, A:K.476 Water bridges: A:S.363 Salt bridges: A:K.476 BGC.11: 9 residues within 4Å: Chain A: F.68, N.69, H.85, Q.331, N.519, A.524, S.525 Ligands: BGC.6, BGC.8 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.69, A:N.69, A:N.519, A:S.525 Water bridges: A:V.83, A:V.83, A:S.525 Salt bridges: A:H.85

1 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.12: 12 residues within 4Å: Chain A: Y.64, G.98, A.100, Q.331, F.416, D.418, V.428, W.430, H.571 Ligands: FAD.3, BGC.7, BGC.8 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:A.100, A:Q.331, A:D.418 Water bridges: A:Y.64, A:Y.64, A:G.98 Salt bridges: A:H.571

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

NAG.13: 2 residues within 4Å: Chain A: V.187, N.188 No protein-ligand interaction detected (PLIP)

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

SO4.14: 3 residues within 4Å: Chain A: G.518, N.519, S.520 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.519 Water bridges: A:S.520 SO4.15: 3 residues within 4Å: Chain A: E.117, K.537, S.539 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.117, A:S.539, A:S.539 Salt bridges: A:K.537 SO4.16: 3 residues within 4Å: Chain A: G.124, N.126, N.129 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.126, A:N.126, A:N.129 SO4.17: 3 residues within 4Å: Chain A: I.155, 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cerutti, G. et al., Crystallographic structure of oligosaccharide dehydrogenase from Pycnoporus cinnabarinus, ligand-free form. To Be Published

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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