SMTL ID : 2f5v.1

Reaction geometry and thermostability mutant of pyranose 2-oxidase from the white-rot fungus Peniophora sp.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.41 Å

Oligo State

homo-tetramer

Ligands

4 x KBG: beta-D-arabino-hexopyranos-2-ulose(Non-covalent)

KBG.1: 11 residues within 4Å: Chain A: T.141, Q.420, H.422, D.424, F.426, R.444, F.446, V.518, H.520, N.565 Ligands: FAD.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.141, A:Q.420, A:Q.420, A:H.422, A:D.424, A:N.565 Water bridges: A:F.426 Salt bridges: A:H.520 KBG.5: 11 residues within 4Å: Chain B: T.141, Q.420, H.422, D.424, F.426, R.444, F.446, V.518, H.520, N.565 Ligands: FAD.6 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:T.141, B:Q.420, B:Q.420, B:H.422, B:D.424, B:N.565 Water bridges: B:F.426 Salt bridges: B:H.520 KBG.9: 11 residues within 4Å: Chain C: T.141, Q.420, H.422, D.424, F.426, R.444, F.446, V.518, H.520, N.565 Ligands: FAD.10 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Q.420, C:Q.420, C:H.422, C:D.424, C:N.565 Water bridges: C:F.426 Salt bridges: C:H.520 KBG.13: 11 residues within 4Å: Chain D: T.141, Q.420, H.422, D.424, F.426, R.444, F.446, V.518, H.520, N.565 Ligands: FAD.14 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:Q.420, D:Q.420, D:H.422, D:D.424, D:N.565 Water bridges: D:F.426 Salt bridges: D:H.520

4 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.2: 34 residues within 4Å: Chain A: V.24, G.25, G.27, P.28, I.29, D.48, I.49, I.79, L.83, T.130, R.131, V.132, G.135, M.136, S.137, H.139, W.140, T.141, C.142, A.143, V.253, A.254, C.255, T.291, A.292, G.293, H.296, L.519, G.554, C.555, N.565, P.566, T.567 Ligands: KBG.1 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:I.79, A:L.83, A:W.140, A:L.519 Hydrogen bonds: A:G.27, A:I.29, A:G.30, A:I.49, A:G.50, A:T.130, A:V.132, A:G.135, A:M.136, A:T.141, A:A.143, A:A.143, A:C.255, A:C.255, A:N.565, A:T.567, A:T.567, A:T.567 Water bridges: A:G.293, A:L.519, A:L.568 pi-Stacking: A:W.140, A:H.520 FAD.6: 34 residues within 4Å: Chain B: V.24, G.25, G.27, P.28, I.29, D.48, I.49, I.79, L.83, T.130, R.131, V.132, G.135, M.136, S.137, H.139, W.140, T.141, C.142, A.143, V.253, A.254, C.255, T.291, A.292, G.293, H.296, L.519, G.554, C.555, N.565, P.566, T.567 Ligands: KBG.5 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:I.79, B:L.83, B:W.140, B:L.519 Hydrogen bonds: B:G.27, B:I.29, B:G.30, B:I.49, B:G.50, B:T.130, B:V.132, B:G.135, B:M.136, B:T.141, B:A.143, B:A.143, B:C.255, B:C.255, B:N.565, B:T.567, B:T.567, B:T.567 Water bridges: B:G.293, B:L.519, B:L.568 pi-Stacking: B:W.140, B:H.520 FAD.10: 34 residues within 4Å: Chain C: V.24, G.25, G.27, P.28, I.29, D.48, I.49, I.79, L.83, T.130, R.131, V.132, G.135, M.136, S.137, H.139, W.140, T.141, C.142, A.143, V.253, A.254, C.255, T.291, A.292, G.293, H.296, L.519, G.554, C.555, N.565, P.566, T.567 Ligands: KBG.9 28 PLIP interactions: 28 interactions with chain C Hydrophobic interactions: C:I.79, C:L.83, C:W.140, C:L.519 Hydrogen bonds: C:G.27, C:I.29, C:G.30, C:I.49, C:G.50, C:T.130, C:V.132, C:G.135, C:M.136, C:T.141, C:T.141, C:A.143, C:A.143, C:C.255, C:C.255, C:N.565, C:T.567, C:T.567, C:T.567 Water bridges: C:G.293, C:L.519, C:L.568 pi-Stacking: C:W.140, C:H.520 FAD.14: 34 residues within 4Å: Chain D: V.24, G.25, G.27, P.28, I.29, D.48, I.49, I.79, L.83, T.130, R.131, V.132, G.135, M.136, S.137, H.139, W.140, T.141, C.142, A.143, V.253, A.254, C.255, T.291, A.292, G.293, H.296, L.519, G.554, C.555, N.565, P.566, T.567 Ligands: KBG.13 28 PLIP interactions: 28 interactions with chain D Hydrophobic interactions: D:I.79, D:L.83, D:W.140, D:L.519 Hydrogen bonds: D:G.27, D:I.29, D:G.30, D:I.49, D:G.50, D:T.130, D:V.132, D:G.135, D:M.136, D:T.141, D:T.141, D:A.143, D:A.143, D:C.255, D:C.255, D:N.565, D:T.567, D:T.567, D:T.567 Water bridges: D:G.293, D:L.519, D:L.568 pi-Stacking: D:W.140, D:H.520

4 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.3: 8 residues within 4Å: Chain A: P.116, E.117, Q.118, D.119, P.120, R.311 Chain D: S.106, T.107 No protein-ligand interaction detected (PLIP) PG4.7: 8 residues within 4Å: Chain B: P.116, E.117, Q.118, D.119, P.120, R.311 Chain C: S.106, T.107 No protein-ligand interaction detected (PLIP) PG4.11: 8 residues within 4Å: Chain B: S.106, T.107 Chain C: P.116, E.117, Q.118, D.119, P.120, R.311 No protein-ligand interaction detected (PLIP) PG4.15: 8 residues within 4Å: Chain A: S.106, T.107 Chain D: P.116, E.117, Q.118, D.119, P.120, R.311 No protein-ligand interaction detected (PLIP)

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 4 residues within 4Å: Chain A: Q.583, N.584, F.585, T.586 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.586 PEG.8: 4 residues within 4Å: Chain B: Q.583, N.584, F.585, T.586 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.586 PEG.12: 4 residues within 4Å: Chain C: Q.583, N.584, F.585, T.586 No protein-ligand interaction detected (PLIP) PEG.16: 4 residues within 4Å: Chain D: Q.583, N.584, F.585, T.586 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bannwarth, M. et al., Reaction Geometry and Thermostable Variant of Pyranose 2-Oxidase from the White-Rot Fungus Peniophora sp. Biochemistry (2006)

Release Date

2006-06-13

Peptides

Pyranose 2-oxidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Pyranose 2-oxidase