SMTL ID : 4mog.1

Pyranose 2-oxidase V546C mutant with 3-fluorinated glucose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x FDA: DIHYDROFLAVINE-ADENINE DINUCLEOTIDE(Covalent)

FDA.1: 32 residues within 4Å: Chain A: V.52, G.53, G.55, P.56, I.57, G.58, F.75, D.76, I.77, I.107, T.158, R.159, V.160, G.163, M.164, H.167, W.168, T.169, C.170, A.171, V.281, C.283, T.319, A.320, H.324, F.454, L.547, C.583, N.593, P.594, T.595 Ligands: G3F.2 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:I.107, A:W.168, A:F.454, A:L.547 Hydrogen bonds: A:S.54, A:G.55, A:I.57, A:G.58, A:I.77, A:G.78, A:T.158, A:V.160, A:G.163, A:M.164, A:T.169, A:A.171, A:A.171, A:C.283, A:C.283, A:N.593, A:T.595, A:T.595, A:T.595 Water bridges: A:A.322, A:L.547 pi-Stacking: A:W.168, A:H.548 FDA.3: 32 residues within 4Å: Chain B: V.52, G.53, G.55, P.56, I.57, G.58, F.75, D.76, I.77, I.107, T.158, R.159, V.160, G.163, M.164, H.167, W.168, T.169, C.170, A.171, V.281, C.283, T.319, A.320, H.324, F.454, L.547, C.583, N.593, P.594, T.595 Ligands: G3F.4 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:I.107, B:W.168, B:F.454, B:L.547 Hydrogen bonds: B:S.54, B:G.55, B:I.57, B:G.58, B:I.77, B:G.78, B:T.158, B:V.160, B:G.163, B:M.164, B:T.169, B:A.171, B:A.171, B:C.283, B:C.283, B:N.593, B:T.595, B:T.595, B:T.595 Water bridges: B:A.322, B:L.547 pi-Stacking: B:W.168, B:H.548 FDA.5: 32 residues within 4Å: Chain C: V.52, G.53, G.55, P.56, I.57, G.58, F.75, D.76, I.77, I.107, T.158, R.159, V.160, G.163, M.164, H.167, W.168, T.169, C.170, A.171, V.281, C.283, T.319, A.320, H.324, F.454, L.547, C.583, N.593, P.594, T.595 Ligands: G3F.6 28 PLIP interactions: 28 interactions with chain C Hydrophobic interactions: C:I.107, C:W.168, C:F.454, C:L.547 Hydrogen bonds: C:S.54, C:G.55, C:I.57, C:G.58, C:I.77, C:G.78, C:T.158, C:V.160, C:G.163, C:M.164, C:T.169, C:A.171, C:A.171, C:C.283, C:C.283, C:N.593, C:T.595, C:T.595, C:T.595 Water bridges: C:A.322, C:H.324, C:L.547 pi-Stacking: C:W.168, C:H.548 FDA.7: 32 residues within 4Å: Chain D: V.52, G.53, G.55, P.56, I.57, G.58, F.75, D.76, I.77, I.107, T.158, R.159, V.160, G.163, M.164, H.167, W.168, T.169, C.170, A.171, V.281, C.283, T.319, A.320, H.324, F.454, L.547, C.583, N.593, P.594, T.595 Ligands: G3F.8 28 PLIP interactions: 28 interactions with chain D Hydrophobic interactions: D:I.107, D:W.168, D:F.454, D:L.547 Hydrogen bonds: D:S.54, D:G.55, D:I.57, D:G.58, D:I.77, D:G.78, D:T.158, D:V.160, D:G.163, D:M.164, D:T.169, D:A.171, D:A.171, D:C.283, D:C.283, D:N.593, D:T.595, D:T.595, D:T.595 Water bridges: D:A.322, D:H.324, D:L.547 pi-Stacking: D:W.168, D:H.548

4 x G3F: 3-deoxy-3-fluoro-beta-D-glucopyranose(Non-covalent)

G3F.2: 12 residues within 4Å: Chain A: T.169, Q.448, H.450, D.452, F.454, Y.456, R.472, F.474, C.546, H.548, N.593 Ligands: FDA.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.169, A:Q.448, A:H.450, A:H.548, A:N.593 Salt bridges: A:H.548 G3F.4: 12 residues within 4Å: Chain B: T.169, Q.448, H.450, D.452, F.454, Y.456, R.472, F.474, C.546, H.548, N.593 Ligands: FDA.3 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.169, B:Q.448, B:H.450, B:H.548, B:N.593 Salt bridges: B:H.548 G3F.6: 12 residues within 4Å: Chain C: T.169, Q.448, H.450, D.452, F.454, Y.456, R.472, F.474, C.546, H.548, N.593 Ligands: FDA.5 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Q.448, C:H.450, C:Y.456, C:H.548, C:N.593 Salt bridges: C:H.548 G3F.8: 12 residues within 4Å: Chain D: T.169, Q.448, H.450, D.452, F.454, Y.456, R.472, F.474, C.546, H.548, N.593 Ligands: FDA.7 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:Q.448, D:H.450, D:Y.456, D:H.548, D:N.593 Salt bridges: D:H.548

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tan, T.C. et al., Structural Basis for Binding of Fluorinated Glucose and Galactose to Trametes multicolor Pyranose 2-Oxidase Variants with Improved Galactose Conversion. Plos One (2014)

Release Date

2014-02-05

Peptides

Pyranose 2-oxidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Pyranose 2-oxidase

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