SMTL ID : 4moe.1

Pyranose 2-oxidase H450G 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: 37 residues within 4Å: Chain A: V.52, G.53, S.54, G.55, P.56, I.57, 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, A.282, C.283, T.319, A.320, G.321, H.324, F.454, L.547, C.583, N.593, P.594, T.595 Ligands: G3F.2 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:I.107, A:L.111, A:F.454, A:L.547 Hydrogen bonds: A:G.55, A:I.57, 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:G.58, A:G.321, A:L.596 pi-Stacking: A:W.168, A:H.548 FDA.6: 32 residues within 4Å: Chain B: V.52, G.53, G.55, P.56, I.57, D.76, I.77, I.107, 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, C.583, N.593, P.594, T.595 Ligands: G3F.7 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: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:G.321, B:G.321, B:L.596 pi-Stacking: B:W.168, B:H.548 FDA.11: 35 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, G.582, C.583, N.593, P.594, T.595 Ligands: G3F.12 29 PLIP interactions: 29 interactions with chain C Hydrophobic interactions: C:I.107, C:L.111, C:F.454, C:L.547 Hydrogen bonds: C:G.53, C:G.55, C:I.57, C:I.77, C:G.78, C:T.158, C:V.160, C:G.163, 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:G.58, C:G.321, C:L.547, C:L.596 pi-Stacking: C:W.168 pi-Cation interactions: C:H.548 FDA.14: 36 residues within 4Å: Chain D: V.52, G.53, G.55, P.56, I.57, 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, G.582, C.583, N.593, P.594, T.595 Ligands: G3F.15 28 PLIP interactions: 28 interactions with chain D Hydrophobic interactions: D:I.107, D:L.111, D:F.454, D:L.547 Hydrogen bonds: D:S.54, D:G.55, D:I.57, D:I.77, D:G.78, D:T.158, D:V.160, 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.58, D:G.321, 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: 11 residues within 4Å: Chain A: T.169, Q.448, D.452, F.454, Y.456, R.472, F.474, V.546, H.548, N.593 Ligands: FDA.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.548, A:N.593 Water bridges: A:D.452, A:D.452 Salt bridges: A:H.548 G3F.7: 11 residues within 4Å: Chain B: T.169, Q.448, D.452, F.454, Y.456, R.472, F.474, V.546, H.548, N.593 Ligands: FDA.6 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.548, B:N.593 Water bridges: B:Q.448, B:D.452 Salt bridges: B:H.548 G3F.12: 11 residues within 4Å: Chain C: T.169, Q.448, D.452, F.454, Y.456, R.472, F.474, V.546, H.548, N.593 Ligands: FDA.11 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Q.448, C:Y.456, C:Y.456, C:H.548, C:N.593 Water bridges: C:D.452 Salt bridges: C:H.548 G3F.15: 11 residues within 4Å: Chain D: T.169, Q.448, D.452, F.454, Y.456, R.472, F.474, V.546, H.548, N.593 Ligands: FDA.14 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:Q.448, D:D.452, D:Y.456, D:Y.456, D:H.548, D:N.593 Salt bridges: D:H.548

4 x 12P: DODECAETHYLENE GLYCOL(Non-covalent)

12P.3: 7 residues within 4Å: Chain A: P.144, Q.146, D.147, P.148 Chain D: S.134, T.135, F.136 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:T.135 12P.5: 6 residues within 4Å: Chain A: S.134, F.136 Chain D: P.144, Q.146, D.147, P.148 No protein-ligand interaction detected (PLIP) 12P.8: 8 residues within 4Å: Chain B: P.144, E.145, Q.146, D.147, P.148 Chain C: S.134, T.135, F.136 No protein-ligand interaction detected (PLIP) 12P.10: 8 residues within 4Å: Chain B: S.134, T.135 Chain C: P.144, E.145, Q.146, D.147, P.148, R.339 1 PLIP interactions: 1 interactions with chain B Water bridges: B:F.136

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

MES.4: 15 residues within 4Å: Chain A: L.121, V.122, V.123, W.131, Q.132, A.133, T.135, F.136, F.137, R.139 Chain B: S.462, I.463, D.464, L.467 Chain D: L.149 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:V.123, B:D.464 Water bridges: A:A.133, A:A.133 Salt bridges: A:R.139 MES.9: 13 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.137, R.139 Chain C: L.149 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:D.464, B:V.123, B:Q.132, B:Q.132, B:A.133 Salt bridges: B:R.139 MES.13: 7 residues within 4Å: Chain C: G.398, A.399, S.400, N.402, K.403, H.404, P.405 No protein-ligand interaction detected (PLIP) MES.16: 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, W.131, Q.132, A.133, T.135, F.137, R.139 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:V.123, D:Q.132, D:Q.132, D:A.133, C:D.464 Salt bridges: D:R.139 MES.17: 7 residues within 4Å: Chain D: G.398, A.399, S.400, N.402, K.403, H.404, P.405 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:H.404, D:H.404 Water bridges: D:D.406

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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