SMTL ID : 3k4m.1 (1 other biounit)

Pyranose 2-oxidase Y456W mutant in complex with 2FG

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

4 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.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, 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, L.547, H.548, G.582, C.583, N.593, P.594, T.595 Ligands: SHG.2 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:I.107, A:L.111, A:W.168, A:L.547 Hydrogen bonds: A:G.55, A:I.57, A:G.58, A:I.77, A:T.158, A:V.160, A:G.163, A:M.164, A:S.165, A:T.169, A:T.169, A:A.171, A:A.171, A:C.283, A:C.283, A:N.593, A:T.595, A:T.595 Water bridges: A:G.321 pi-Stacking: A:W.168 FAD.4: 33 residues within 4Å: Chain B: V.52, G.53, G.55, P.56, I.57, D.76, I.77, G.78, 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, L.547, G.582, C.583, N.593, P.594, T.595 Ligands: SHG.5 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:I.107, B:W.168, B:L.547 Hydrogen bonds: B:S.54, B:G.55, B:I.57, B:I.77, B:G.78, B:V.160, B:M.164, B:M.164, B:S.165, B:T.169, B:A.171, B:A.171, B:C.283, B:C.283, B:N.593, B:T.595, B:T.595 Water bridges: B:G.58, B:A.322, B:L.547, B:L.596 pi-Stacking: B:W.168, B:W.168, B:H.548 pi-Cation interactions: B:H.548 FAD.7: 33 residues within 4Å: Chain C: V.52, G.53, G.55, P.56, I.57, G.58, F.75, D.76, I.77, 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, L.547, G.582, C.583, N.593, P.594, T.595 Ligands: SHG.8 26 PLIP interactions: 26 interactions with chain C Hydrophobic interactions: C:W.168, C:L.547 Hydrogen bonds: C:I.57, C:G.58, C:I.77, C:G.78, C:V.160, C:V.160, C:M.164, C:S.165, C:T.169, C:T.169, C:C.170, C:A.171, C:A.171, C:C.283, C:C.283, C:N.593, C:T.595, C:T.595 Water bridges: C:G.55, C:G.321, C:L.547 pi-Stacking: C:W.168 pi-Cation interactions: C:H.548, C:H.548 FAD.11: 34 residues within 4Å: Chain D: V.52, G.53, S.54, G.55, P.56, I.57, D.76, I.77, G.78, 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, L.547, H.548, G.582, C.583, N.593, P.594, T.595 Ligands: SHG.12 27 PLIP interactions: 27 interactions with chain D Hydrophobic interactions: D:W.168, D:L.547 Hydrogen bonds: D:G.55, D:I.57, D:I.77, D:G.78, D:V.160, D:V.160, D:G.163, D:M.164, D:M.164, D:T.169, D:T.169, D:C.170, D:A.171, D:A.171, D:C.283, D:C.283, D:N.593, D:T.595, D:T.595 Water bridges: D:G.58, D:G.321, D:L.547, D:L.596 pi-Stacking: D:W.168, D:H.548

4 x SHG: 2-deoxy-2-fluoro-beta-D-glucopyranose(Non-covalent)

SHG.2: 11 residues within 4Å: Chain A: T.169, A.171, Q.448, H.450, D.452, R.472, F.474, V.546, H.548, N.593 Ligands: FAD.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.448, A:H.548, A:N.593 Salt bridges: A:H.450, A:R.472 SHG.5: 11 residues within 4Å: Chain B: T.169, A.171, Q.448, H.450, D.452, R.472, F.474, V.546, H.548, N.593 Ligands: FAD.4 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.448, B:H.548, B:N.593 Salt bridges: B:H.450, B:R.472 SHG.8: 10 residues within 4Å: Chain C: T.169, Q.448, H.450, D.452, R.472, F.474, V.546, H.548, N.593 Ligands: FAD.7 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:Q.448, C:D.452, C:L.545, C:H.548, C:N.593 Water bridges: C:R.472 Salt bridges: C:H.450, C:R.472 SHG.12: 10 residues within 4Å: Chain D: T.169, A.171, Q.448, H.450, D.452, R.472, V.546, H.548, N.593 Ligands: FAD.11 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Q.448, D:H.548, D:N.593 Salt bridges: D:H.450, D:R.472

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

MES.3: 13 residues within 4Å: Chain A: L.121, V.122, V.123, W.131, Q.132, A.133, T.135, F.137, R.139 Chain B: S.462, I.463, D.464 Chain D: L.149 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:V.123, A:Q.132, A:Q.132, A:A.133, B:S.462, B:D.464 Salt bridges: A:R.139 MES.6: 12 residues within 4Å: Chain A: S.462, I.463, D.464, L.467 Chain B: L.121, V.122, V.123, A.133, F.136, F.137, R.139 Chain C: L.149 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:V.123, B:A.133, A:D.464 MES.9: 12 residues within 4Å: Chain B: L.149 Chain C: L.121, V.123, W.131, A.133, T.135, F.136, F.137, R.139 Chain D: S.462, I.463, D.464 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:D.464, C:V.123, C:A.133 MES.10: 13 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, A.133, F.136, F.137, R.139 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:V.123, D:A.133, C:D.464

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Spadiut, O. et al., Importance of the gating segment in the substrate-recognition loop of pyranose 2-oxidase. Febs J. (2010)

Release Date

2010-05-12

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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