SMTL ID : 7vkf.1

Reduced enzyme of FAD-dpendent Glucose Dehydrogenase complex with D-glucono-1,5-lactone at pH8.5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x LGC: D-glucono-1,5-lactone(Non-covalent)

LGC.1: 12 residues within 4Å: Chain A: Y.54, G.95, A.97, N.319, L.402, E.414, W.416, R.502, N.504, H.506, H.549 Ligands: FDA.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Y.54, A:N.319, A:E.414, A:E.414, A:R.502, A:R.502, A:H.506, A:H.549 Salt bridges: A:H.549

1 x FDA: DIHYDROFLAVINE-ADENINE DINUCLEOTIDE(Non-covalent)

FDA.2: 40 residues within 4Å: Chain A: G.13, G.14, G.15, T.16, S.17, L.36, E.37, A.38, Y.54, F.58, W.64, R.82, G.84, K.85, A.86, G.89, T.90, S.91, I.93, N.94, G.95, M.96, A.97, T.234, T.235, A.236, S.275, A.276, G.277, R.280, I.284, F.505, H.506, D.538, A.539, H.549, L.550, V.551, L.554 Ligands: LGC.1 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:F.58, A:T.90, A:F.505, A:F.505 Hydrogen bonds: A:G.14, A:T.16, A:T.16, A:S.17, A:A.38, A:G.84, A:A.86, A:T.90, A:T.90, A:N.94, A:G.95, A:A.97, A:A.97, A:A.236, A:A.236, A:A.539, A:H.549, A:L.550, A:V.551 Water bridges: A:G.15, A:G.18, A:G.84, A:T.90, A:A.278, A:R.280, A:F.505, A:S.552

1 x B3P: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

B3P.3: 5 residues within 4Å: Chain A: F.220, P.221, Y.222, D.223, D.224 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.223, A:D.224 Water bridges: A:P.221, A:D.224, A:R.225

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakajima, Y., Conformational change of catalytic residue in reduced enzyme of FAD-dependent Glucose Dehydrogenase at pH6.5. To Be Published

Release Date

2022-10-05

Peptides

GMC oxidoreductase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GMC oxidoreductase

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