SMTL ID : 8ate.1

Galacturonic acid oxidase from Citrus sinensis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

monomer

Ligands

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.1: 30 residues within 4Å: Chain A: I.84, R.85, S.86, G.87, G.88, H.89, D.90, Y.91, S.95, M.107, T.126, G.149, V.150, C.151, V.154, G.155, G.157, G.158, H.159, G.164, Y.165, G.210, A.211, G.214, V.215, V.216, F.449, N.451, R.453 Ligands: CL.3 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:H.89, A:Y.91, A:V.154 Hydrogen bonds: A:I.84, A:S.86, A:S.86, A:G.87, A:G.88, A:H.89, A:D.90, A:D.90, A:S.95, A:S.95, A:V.150, A:G.155, A:G.155, A:G.158, A:H.159, A:Y.165, A:Y.165, A:V.216, A:V.216, A:N.451, A:N.451, A:N.451, A:R.453 Water bridges: A:R.265 pi-Stacking: A:H.159

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

NAG.2: 3 residues within 4Å: Chain A: Q.40, L.46, N.49 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.40, A:N.49

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

CL.3: 3 residues within 4Å: Chain A: Y.91, R.351 Ligands: FAD.1 Ligand excluded by PLIP

2 x IOD: IODIDE ION(Non-functional Binders)

IOD.4: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.5: 2 residues within 4Å: Chain A: K.370, R.371 Ligand excluded by PLIP

2 x NA: SODIUM ION(Non-functional Binders)

NA.6: 1 residues within 4Å: Chain A: S.303 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.303, A:S.303 NA.7: 2 residues within 4Å: Chain A: S.36, K.55 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 8 residues within 4Å: Chain A: R.170, S.255, K.256, Q.257, L.258, P.259, D.260, G.387 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.170, A:D.260, A:G.387 Water bridges: A:K.256

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

PEG.9: 6 residues within 4Å: Chain A: K.352, R.431, Y.434, D.456, L.457, K.476 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.352, A:R.431

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Boverio, A. et al., Biochemical and Structural Characterization of a Uronic Acid Oxidase from Citrus sinensis. Chemcatchem (2023)

Release Date

2023-09-06

Peptides

FAD-binding PCMH-type domain-containing protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

FAD-binding PCMH-type domain-containing protein