SMTL ID : 5zu3.1 (2 other biounits)

Effect of mutation (R554K) on FAD modification in Aspergillus oryzae RIB40formate oxidase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 x FAY: [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-(8-formyl-7-methyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)-2,3,4-trihydroxypentyl dihydrogen diphosphate(Non-covalent)

FAY.1: 35 residues within 4Å: Chain A: G.13, G.14, G.15, T.16, A.17, E.37, A.38, W.65, T.85, R.86, G.87, K.88, T.89, G.92, S.93, S.94, L.96, N.97, Y.98, F.99, T.100, V.227, H.228, S.229, S.265, Q.266, G.267, E.270, F.509, D.542, A.543, K.553, I.554, Q.555, V.558 37 PLIP interactions: 37 interactions with chain A Hydrophobic interactions: A:T.85, A:Y.98, A:F.509, A:F.509 Hydrogen bonds: A:T.16, A:T.16, A:A.17, A:A.38, A:R.86, A:T.89, A:T.89, A:S.93, A:S.93, A:S.93, A:N.97, A:Y.98, A:T.100, A:T.100, A:S.229, A:Q.266, A:E.270, A:A.543, A:I.554, A:Q.555, A:Q.555 Water bridges: A:G.15, A:G.18, A:V.268, A:V.268, A:V.268, A:K.273, A:K.273, A:K.553, A:K.553, A:N.556 pi-Stacking: A:Y.98 pi-Cation interactions: A:H.510

3 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.2: 6 residues within 4Å: Chain A: Y.468, D.469, F.472, K.473, E.484, L.491 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.468, A:L.491 Hydrogen bonds: A:D.469, A:E.484 MPD.3: 2 residues within 4Å: Chain A: H.6, D.259 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.6 MPD.4: 5 residues within 4Å: Chain A: K.230, E.253, D.439, P.440, F.441 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:D.439, A:P.440, A:F.441 Hydrogen bonds: A:D.439, A:F.441

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 9 residues within 4Å: Chain A: W.65, Y.67, H.228, E.270, K.273, P.440, F.441, Q.442, Q.443 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.65 Salt bridges: A:H.228, A:K.273

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Doubayashi, D. et al., The microenvironment surrounding FAD mediates its conversion to 8-formyl-FAD in Aspergillus oryzae RIB40 formate oxidase. J.Biochem. (2019)

Release Date

2019-05-22

Peptides

Formate oxidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Formate oxidase

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