SMTL ID : 4xwz.1

The crystal structure of Fructosyl amine: oxygen oxidoreductase (Amadoriase I) from Aspergillus fumigatus in complex with the substrate fructosyl lysine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 35 residues within 4Å: Chain A: I.31, G.32, A.33, G.34, T.35, W.36, L.55, D.56, P.57, H.58, S.62, I.64, A.65, A.66, G.67, K.72, I.73, G.206, N.207, V.208, A.238, G.239, L.245, W.257, C.358, W.359, D.360, G.385, G.387, N.388, G.389, A.390, M.391 Ligands: LYS.2, BDF.3 29 PLIP interactions: 1 Ligand-Ligand interactions, 28 interactions with chain A Hydrogen bonds: K.2, A:A.33, A:T.35, A:T.35, A:W.36, A:S.62, A:S.62, A:A.66, A:G.67, A:K.72, A:I.73, A:I.73, A:V.208, A:V.208, A:G.239, A:D.360, A:N.388, A:G.389, A:A.390, A:M.391 Hydrophobic interactions: A:W.257 Water bridges: A:G.34, A:G.37, A:S.62, A:A.240, A:A.240, A:G.241 pi-Cation interactions: A:K.72, A:K.72 FAD.4: 35 residues within 4Å: Chain B: I.31, G.32, A.33, G.34, T.35, W.36, L.55, D.56, P.57, H.58, S.62, I.64, A.65, A.66, G.67, K.72, I.73, G.206, N.207, V.208, A.238, G.239, L.245, W.257, C.358, W.359, D.360, G.385, G.387, N.388, G.389, A.390, M.391 Ligands: LYS.5, BDF.6 29 PLIP interactions: 29 interactions with chain B Hydrophobic interactions: B:W.257 Hydrogen bonds: B:A.33, B:T.35, B:T.35, B:W.36, B:S.62, B:S.62, B:I.64, B:A.66, B:G.67, B:K.72, B:I.73, B:I.73, B:V.208, B:V.208, B:G.239, B:D.360, B:N.388, B:G.389, B:A.390, B:M.391 Water bridges: B:G.34, B:G.37, B:S.62, B:S.62, B:A.240, B:G.241 pi-Cation interactions: B:K.72, B:K.72

2 x LYS: LYSINE(Non-covalent)

LYS.2: 10 residues within 4Å: Chain A: I.73, E.75, F.91, F.117, F.285, G.387, N.388, M.391 Ligands: FAD.1, BDF.3 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.73 Hydrogen bonds: A:N.388 LYS.5: 9 residues within 4Å: Chain B: I.73, E.75, F.91, F.117, G.387, N.388, M.391 Ligands: FAD.4, BDF.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.75, B:G.387, B:N.388

2 x BDF: beta-D-fructopyranose(Non-covalent)

BDF.3: 8 residues within 4Å: Chain A: W.257, F.285, E.301, R.366, G.387, R.434 Ligands: FAD.1, LYS.2 9 PLIP interactions: 2 Ligand-Ligand interactions, 7 interactions with chain A Hydrophobic interactions: K.2, A:F.285 Hydrogen bonds: K.2, A:E.301, A:R.434, A:R.434 Water bridges: A:R.366, A:R.366, A:R.366 BDF.6: 8 residues within 4Å: Chain B: W.257, F.285, E.301, R.366, G.387, R.434 Ligands: FAD.4, LYS.5 9 PLIP interactions: 6 interactions with chain B, 3 Ligand-Ligand interactions Hydrophobic interactions: B:F.285, K.5 Hydrogen bonds: B:E.301, B:R.434, B:R.434, K.5 Water bridges: B:R.366, B:R.366, K.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rigoldi, F. et al., Crystal structure of the deglycating enzyme Amadoriase I in its free form and substrate-bound complex. Proteins (2016)

Release Date

2016-02-10

Peptides

Fructosyl amine:oxygen oxidoreductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Fructosyl amine:oxygen oxidoreductase

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