SMTL ID : 7vzs.2 (1 other biounit)

FAD-dpendent Glucose Dehydrogenase complexed with an inhibitor at pH7.56

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

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

FAD.1: 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, D.538, A.539, H.549, L.550, V.551, L.554 Ligands: DGO.2, 1PE.8 30 PLIP interactions: 30 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:L.550, A:V.551 Water bridges: A:G.15, A:G.18, A:G.84, A:G.84, A:A.278, A:A.278, A:F.505, A:S.552

5 x DGO: D-glucal(Non-covalent)

DGO.2: 9 residues within 4Å: Chain A: Y.54, G.95, N.319, L.402, E.414, R.502, N.504, H.549 Ligands: FAD.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.319, A:E.414, A:R.502, A:R.502 DGO.3: 7 residues within 4Å: Chain A: Y.9, R.24, L.25, N.28, V.31, K.566, A.569 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.9, A:L.25, A:K.566 Hydrogen bonds: A:N.28, A:N.28 Water bridges: A:K.566, A:K.566 DGO.4: 8 residues within 4Å: Chain A: I.352, S.355, L.356, Q.359, Y.363, E.447, W.448, K.451 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.352, A:K.451 Hydrogen bonds: A:S.355, A:Q.359, A:Q.359, A:Y.363, A:E.447, A:E.447, A:K.451 DGO.5: 4 residues within 4Å: Chain A: V.140, A.145, Y.146, P.148 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.140 Hydrogen bonds: A:Y.146 Water bridges: A:E.187 DGO.6: 7 residues within 4Å: Chain A: A.141, A.142, G.143, S.167, S.171, V.172, N.175 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.141, A:N.175 Water bridges: A:S.171

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

SO4.7: 4 residues within 4Å: Chain A: R.516, R.527, Y.529, G.530 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.530 Salt bridges: A:R.516, A:R.527

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.8: 13 residues within 4Å: Chain A: W.64, Q.65, Y.66, A.236, N.237, R.280, L.283, I.284, L.287, P.433, T.434, A.435 Ligands: FAD.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.67

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

2022-11-16

Peptides

GMC oxidoreductase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

GMC oxidoreductase

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