SMTL ID : 3lsk.1

Pyranose 2-oxidase T169S acetate complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

4 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.1: 34 residues within 4Å: Chain A: 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, S.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, N.593, P.594, T.595 Ligands: ACT.2 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:I.107, A:W.168, A:F.454, A:L.547 Hydrogen bonds: A:G.55, A:I.57, A:G.58, A:I.77, A:G.78, A:V.160, A:V.160, A:M.164, A:S.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.321, A:L.596 pi-Stacking: A:W.168 pi-Cation interactions: A:H.548 FAD.5: 34 residues within 4Å: Chain B: V.52, G.53, G.55, P.56, I.57, F.75, D.76, I.77, G.78, I.107, T.158, R.159, V.160, G.163, M.164, S.165, H.167, W.168, S.169, C.170, A.171, V.281, A.282, C.283, T.319, A.320, G.321, H.324, L.547, C.583, N.593, P.594, T.595 Ligands: ACT.6 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:I.107, B:W.168, B:L.547 Hydrogen bonds: B:G.55, B:I.57, B:I.77, B:G.78, B:V.160, B:V.160, B:G.162, B:G.163, B:M.164, B:S.165, B:S.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.58, B:G.321, B:Q.448, B:L.596 pi-Stacking: B:W.168 pi-Cation interactions: B:H.548 FAD.8: 33 residues within 4Å: Chain C: V.52, G.53, 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, S.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: ACT.9 29 PLIP interactions: 29 interactions with chain C Hydrophobic interactions: C:W.168, C:F.454, C:F.454, C:L.547 Hydrogen bonds: C:I.57, C:I.77, C:G.78, C:T.158, C:V.160, C:M.164, C:M.164, C:S.165, C:S.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.55, C:G.55, C:G.321, C:H.324, C:Q.448, C:L.596 pi-Stacking: C:W.168 pi-Cation interactions: C:H.548 FAD.11: 33 residues within 4Å: Chain D: 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, S.169, C.170, A.171, V.281, C.283, T.319, A.320, G.321, H.324, L.547, H.548, C.583, N.593, P.594, T.595 Ligands: ACT.12 24 PLIP interactions: 24 interactions with chain D Hydrophobic interactions: D:I.107, D:W.168, D:L.547 Hydrogen bonds: D:G.55, D:I.57, D:I.77, D:G.78, D:T.158, D:G.163, D:M.164, D:S.165, D:S.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:L.547 pi-Stacking: D:W.168, D:H.548

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 7 residues within 4Å: Chain A: S.169, Q.448, F.454, F.474, H.548, N.593 Ligands: FAD.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.454 Hydrogen bonds: A:N.593 Salt bridges: A:H.548 ACT.6: 7 residues within 4Å: Chain B: S.169, Q.448, F.454, F.474, H.548, N.593 Ligands: FAD.5 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.454, B:F.474 Hydrogen bonds: B:N.593 Water bridges: B:R.472 Salt bridges: B:H.548 ACT.9: 6 residues within 4Å: Chain C: S.169, Q.448, F.454, H.548, N.593 Ligands: FAD.8 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.454 Hydrogen bonds: C:N.593 Salt bridges: C:H.548 ACT.12: 7 residues within 4Å: Chain D: S.169, Q.448, F.454, F.474, H.548, N.593 Ligands: FAD.11 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:F.454, D:F.474 Hydrogen bonds: D:N.593 Salt bridges: D:H.548

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

12P.3: 8 residues within 4Å: Chain A: P.144, E.145, Q.146, D.147, P.148, R.339 Chain C: S.134, T.135 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.147 12P.4: 9 residues within 4Å: Chain A: S.134, T.135, F.136 Chain C: P.144, E.145, Q.146, D.147, P.148, R.339 1 PLIP interactions: 1 interactions with chain C Water bridges: C:E.145 12P.7: 8 residues within 4Å: Chain B: P.144, E.145, Q.146, D.147, P.148, R.339 Chain D: S.134, T.135 No protein-ligand interaction detected (PLIP) 12P.10: 7 residues within 4Å: Chain C: R.288, N.289, A.290, N.292, G.333, E.347, L.348 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.288, C:R.288, C:N.292 12P.13: 7 residues within 4Å: Chain B: S.134, F.136 Chain D: P.144, E.145, Q.146, D.147, P.148 No protein-ligand interaction detected (PLIP) 12P.14: 6 residues within 4Å: Chain D: R.288, N.289, A.290, N.292, G.333, E.347 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.288, D:R.288, D:N.292 Water bridges: D:R.288, D:R.288

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tan, T.C. et al., H-bonding and positive charge at the N5/O4 locus are critical for covalent flavin attachment in trametes pyranose 2-oxidase. J.Mol.Biol. (2010)

Release Date

2010-08-25

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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