SMTL ID : 4moj.1

Pyranose 2-oxidase H450G/V546C double mutant with 2-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: 37 residues within 4Å: Chain A: V.52, G.53, G.55, P.56, I.57, G.58, D.76, I.77, G.78, I.107, L.111, T.158, R.159, V.160, G.163, M.164, S.165, H.167, W.168, T.169, C.170, A.171, V.281, A.282, C.283, T.319, A.320, G.321, H.324, F.454, L.547, H.548, C.583, N.593, P.594, T.595 Ligands: G2F.2 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:I.107, A:L.111, A:W.168, A:F.454, A:L.547 Hydrogen bonds: A:I.57, A:G.58, A:I.77, A:G.78, A:T.158, A:V.160, A:M.164, A:M.164, A:S.165, 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:G.55, A:L.547, A:L.596 pi-Stacking: A:W.168 pi-Cation interactions: A:H.548 FDA.6: 38 residues within 4Å: Chain B: V.52, G.53, G.55, P.56, I.57, G.58, F.75, D.76, I.77, G.78, I.107, L.111, T.158, R.159, V.160, G.163, M.164, S.165, H.167, W.168, T.169, C.170, A.171, V.281, C.283, T.319, A.320, G.321, H.324, F.454, L.547, H.548, G.582, C.583, N.593, P.594, T.595 Ligands: G2F.7 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:I.107, B:L.111, B:F.454, B:L.547 Hydrogen bonds: 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:L.547, B:L.596 pi-Stacking: B:W.168, B:H.548 FDA.9: 36 residues within 4Å: Chain C: V.52, G.53, G.55, P.56, I.57, F.75, D.76, I.77, I.107, L.111, T.158, R.159, V.160, G.163, M.164, S.165, H.167, W.168, T.169, C.170, A.171, V.281, C.283, T.319, A.320, G.321, H.324, F.454, L.547, H.548, G.582, C.583, N.593, P.594, T.595 Ligands: G2F.10 28 PLIP interactions: 28 interactions with chain C Hydrophobic interactions: C:I.107, C:L.111, 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:T.158, C:V.160, C:M.164, C:M.164, C:T.169, 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:L.547, C:L.596 pi-Stacking: C:W.168, C:W.168 FDA.12: 34 residues within 4Å: Chain D: V.52, G.53, G.55, P.56, I.57, D.76, I.77, L.111, T.158, R.159, V.160, G.163, M.164, S.165, H.167, W.168, T.169, C.170, A.171, V.281, C.283, T.319, A.320, G.321, H.324, F.454, L.547, H.548, G.582, C.583, N.593, P.594, T.595 Ligands: G2F.13 28 PLIP interactions: 28 interactions with chain D Hydrophobic interactions: D:L.111, D:F.454, D:L.547 Hydrogen bonds: 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:S.165, D:T.169, 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:G.321, D:L.547, D:L.596 pi-Stacking: D:W.168 pi-Cation interactions: D:H.548

4 x G2F: 2-deoxy-2-fluoro-alpha-D-glucopyranose(Non-covalent)

G2F.2: 13 residues within 4Å: Chain A: T.169, L.361, Q.448, D.452, F.454, Y.456, R.472, F.474, L.545, C.546, H.548, N.593 Ligands: FDA.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.169, A:T.169, A:L.545, A:H.548, A:N.593 Water bridges: A:F.454 Salt bridges: A:R.472 G2F.7: 13 residues within 4Å: Chain B: T.169, L.361, Q.448, D.452, F.454, Y.456, R.472, F.474, L.545, C.546, H.548, N.593 Ligands: FDA.6 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:T.169, B:T.169, B:L.545, B:H.548, B:N.593 Water bridges: B:F.454 Salt bridges: B:R.472 G2F.10: 13 residues within 4Å: Chain C: T.169, L.361, Q.448, D.452, F.454, Y.456, R.472, F.474, L.545, C.546, H.548, N.593 Ligands: FDA.9 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:T.169, C:Y.456, C:L.545, C:H.548, C:N.593 Water bridges: C:Q.448 Salt bridges: C:R.472 G2F.13: 13 residues within 4Å: Chain D: T.169, L.361, Q.448, D.452, F.454, Y.456, R.472, F.474, L.545, C.546, H.548, N.593 Ligands: FDA.12 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:T.169, D:Y.456, D:L.545, D:H.548, D:N.593 Water bridges: D:D.452, D:A.453 Salt bridges: D:R.472

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

1PE.3: 5 residues within 4Å: Chain A: P.144, Q.146, D.147, P.148 Chain D: S.134 No protein-ligand interaction detected (PLIP) 1PE.8: 8 residues within 4Å: Chain B: P.144, E.145, Q.146, D.147, P.148, R.339 Chain C: S.134, T.135 No protein-ligand interaction detected (PLIP) 1PE.11: 7 residues within 4Å: Chain B: S.134, T.135 Chain C: P.144, E.145, Q.146, D.147, P.148 1 PLIP interactions: 1 interactions with chain B Water bridges: B:F.136 1PE.14: 7 residues within 4Å: Chain A: S.134, T.135 Chain D: P.144, E.145, Q.146, D.147, P.148 1 PLIP interactions: 1 interactions with chain D Water bridges: D:E.145

4 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.4: 7 residues within 4Å: Chain A: G.398, A.399, N.402, K.403, H.404, P.405, D.406 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.403, A:H.404 MES.5: 14 residues within 4Å: Chain A: S.462, I.463, D.464 Chain B: L.121, V.122, V.123, W.131, Q.132, A.133, T.135, F.136, F.137, R.139 Chain C: L.149 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:V.123, B:Q.132, B:Q.132, B:Q.132, B:A.133, A:S.462, A:S.462, A:D.464 Salt bridges: B:R.139 MES.15: 14 residues within 4Å: Chain A: L.149 Chain C: S.462, I.463, D.464, L.467 Chain D: L.121, V.122, V.123, L.126, W.131, Q.132, A.133, F.137, R.139 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:V.123, D:A.133, C:S.462, C:S.462, C:D.464 Salt bridges: D:R.139 MES.16: 7 residues within 4Å: Chain D: G.398, A.399, S.400, N.402, K.403, H.404, P.405 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.404

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
B

C
C

D
D

Pyranose 2-oxidase

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