SMTL ID : 4mig.1

Pyranose 2-oxidase from Phanerochaete chrysosporium, recombinant wild type

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

4 x FDA: DIHYDROFLAVINE-ADENINE DINUCLEOTIDE(Covalent)

FDA.1: 36 residues within 4Å: Chain A: G.34, G.36, P.37, I.38, V.56, E.57, I.58, I.110, T.163, R.164, G.165, G.168, M.169, S.170, H.172, W.173, T.174, C.175, A.176, H.295, R.296, C.297, A.345, C.346, G.347, A.350, V.354, F.474, L.566, H.567, G.599, N.600, N.610, P.611, T.612 Ligands: G3F.2 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:I.110, A:W.173, A:F.474, A:L.566 Hydrogen bonds: A:G.36, A:I.38, A:I.58, A:T.163, A:G.165, A:G.168, A:M.169, A:T.174, A:T.174, A:A.176, A:A.176, A:C.297, A:C.297, A:N.600, A:N.610, A:T.612, A:T.612 Water bridges: A:G.39, A:G.347, A:G.347, A:A.348, A:N.600, A:L.613 pi-Stacking: A:W.173 FDA.6: 37 residues within 4Å: Chain B: G.34, G.36, P.37, I.38, V.56, E.57, I.58, I.110, L.114, T.163, R.164, G.165, G.168, M.169, S.170, H.172, W.173, T.174, C.175, A.176, H.295, R.296, C.297, A.345, C.346, G.347, A.350, V.354, F.474, L.566, H.567, G.599, N.600, N.610, P.611, T.612 Ligands: G3F.7 31 PLIP interactions: 31 interactions with chain B Hydrophobic interactions: B:I.110, B:L.114, B:W.173, B:F.474, B:L.566 Hydrogen bonds: B:G.36, B:I.38, B:I.58, B:T.163, B:G.165, B:G.168, B:M.169, B:T.174, B:T.174, B:A.176, B:A.176, B:C.297, B:C.297, B:N.600, B:N.610, B:T.612, B:T.612, B:T.612 Water bridges: B:G.39, B:G.347, B:G.347, B:A.348, B:L.613 pi-Stacking: B:W.173, B:W.173, B:H.567 FDA.9: 36 residues within 4Å: Chain C: G.34, G.36, P.37, I.38, V.56, E.57, I.58, I.110, T.163, R.164, G.165, G.168, M.169, S.170, H.172, W.173, T.174, C.175, A.176, H.295, R.296, C.297, A.345, C.346, G.347, A.350, V.354, F.474, L.566, H.567, G.599, N.600, N.610, P.611, T.612 Ligands: G3F.10 31 PLIP interactions: 31 interactions with chain C Hydrophobic interactions: C:I.110, C:W.173, C:F.474, C:L.566 Hydrogen bonds: C:S.35, C:G.36, C:I.38, C:I.58, C:T.163, C:G.165, C:G.168, C:M.169, C:T.174, C:T.174, C:T.174, C:A.176, C:A.176, C:C.297, C:C.297, C:N.600, C:N.610, C:T.612, C:T.612, C:T.612 Water bridges: C:G.39, C:G.347, C:G.347, C:A.348, C:L.613 pi-Stacking: C:W.173, C:H.567 FDA.12: 37 residues within 4Å: Chain D: G.34, G.36, P.37, I.38, V.56, E.57, I.58, I.110, L.114, T.163, R.164, G.165, G.168, M.169, S.170, H.172, W.173, T.174, C.175, A.176, H.295, R.296, C.297, A.345, C.346, G.347, A.350, V.354, F.474, L.566, H.567, G.599, N.600, N.610, P.611, T.612 Ligands: G3F.13 33 PLIP interactions: 33 interactions with chain D Hydrophobic interactions: D:I.110, D:L.114, D:W.173, D:F.474, D:L.566 Hydrogen bonds: D:S.35, D:G.36, D:I.38, D:I.58, D:T.163, D:G.165, D:G.167, D:G.168, D:M.169, D:M.169, D:T.174, D:T.174, D:A.176, D:A.176, D:C.297, D:C.297, D:N.600, D:N.610, D:T.612, D:T.612 Water bridges: D:G.39, D:G.347, D:G.347, D:A.348, D:N.600, D:L.613 pi-Stacking: D:W.173 pi-Cation interactions: D:H.567

4 x G3F: 3-deoxy-3-fluoro-beta-D-glucopyranose(Non-covalent)

G3F.2: 12 residues within 4Å: Chain A: T.174, Q.468, H.470, D.472, F.474, Y.476, R.492, F.494, A.565, H.567, N.610 Ligands: FDA.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.174, A:T.174, A:Q.468, A:H.567, A:N.610 Salt bridges: A:H.567 G3F.7: 12 residues within 4Å: Chain B: T.174, Q.468, H.470, D.472, F.474, Y.476, R.492, F.494, A.565, H.567, N.610 Ligands: FDA.6 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.174, B:Q.468, B:H.567, B:N.610 Salt bridges: B:H.567 G3F.10: 12 residues within 4Å: Chain C: T.174, Q.468, H.470, D.472, F.474, Y.476, R.492, F.494, A.565, H.567, N.610 Ligands: FDA.9 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Q.468, C:H.470, C:Y.476, C:H.567, C:N.610 Salt bridges: C:H.567 G3F.13: 12 residues within 4Å: Chain D: T.174, Q.468, H.470, D.472, F.474, Y.476, R.492, F.494, A.565, H.567, N.610 Ligands: FDA.12 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Q.468, D:H.470, D:H.567, D:N.610 Salt bridges: D:H.567

8 x MN: MANGANESE (II) ION(Non-covalent)

MN.3: 1 residues within 4Å: Chain A: H.586 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.586, H2O.1, H2O.1 MN.4: 2 residues within 4Å: Chain A: I.206, R.621 No protein-ligand interaction detected (PLIP) MN.5: 2 residues within 4Å: Chain A: F.524, P.562 No protein-ligand interaction detected (PLIP) MN.8: 2 residues within 4Å: Chain B: F.524, P.562 No protein-ligand interaction detected (PLIP) MN.11: 1 residues within 4Å: Chain C: F.524 No protein-ligand interaction detected (PLIP) MN.14: 1 residues within 4Å: Chain D: H.586 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.586, H2O.46, H2O.46 MN.15: 1 residues within 4Å: Chain D: R.621 No protein-ligand interaction detected (PLIP) MN.16: 1 residues within 4Å: Chain D: F.524 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hassan, N. et al., Crystal structures of Phanerochaete chrysosporium pyranose 2-oxidase suggest that the N-terminus acts as a propeptide that assists in homotetramer assembly. FEBS Open Bio (2013)

Release Date

2013-12-11

Peptides

Pyranose 2-oxidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pyranose 2-oxidase