SMTL ID : 1juh.2 (1 other biounit)

Crystal Structure of Quercetin 2,3-dioxygenase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.1: 7 residues within 4Å: Chain A: V.190, N.191 Chain B: Q.83, W.85, T.187, D.188, T.189 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.187, B:T.189, B:T.189 Hydrophobic interactions: B:W.85

6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 2 residues within 4Å: Chain A: R.108, N.109 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.109 Water bridges: A:Q.69, A:Q.69 NAG.3: 5 residues within 4Å: Chain A: N.248, G.272, S.325, G.326 Ligands: EDO.12 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.248 Water bridges: A:P.271, A:A.273, A:S.325, A:S.325 NAG.4: 2 residues within 4Å: Chain A: R.26, N.142 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.26, A:N.142 NAG.15: 3 residues within 4Å: Chain B: Q.69, R.108, N.109 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.109 Water bridges: B:Q.69 NAG.16: 4 residues within 4Å: Chain B: N.142, A.143, T.144 Ligands: EDO.23 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.142, B:T.144, B:T.144 Water bridges: B:D.145 NAG.17: 4 residues within 4Å: Chain B: N.248, G.272, S.325, G.326 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.248 Water bridges: B:P.271, B:A.273, B:S.325, B:S.325

2 x CU: COPPER (II) ION(Non-covalent)

CU.5: 4 residues within 4Å: Chain A: H.66, H.68, E.73, H.112 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.66, A:H.68, A:H.112, H2O.11 CU.18: 4 residues within 4Å: Chain B: H.66, H.68, E.73, H.112 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.66, B:H.68, B:H.112, H2O.28

13 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 7 residues within 4Å: Chain A: Y.72, P.107, R.108, G.212, Q.243, A.244, Q.245 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.108, A:R.108 EDO.7: 7 residues within 4Å: Chain A: M.51, E.73, N.74, F.75, M.123, G.125, I.127 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.53, A:T.53, A:N.74 Water bridges: A:G.125 EDO.8: 2 residues within 4Å: Chain A: T.92, N.197 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.92, A:T.92, A:N.197 Water bridges: A:Q.94, A:N.197 EDO.9: 7 residues within 4Å: Chain A: S.228, Q.229, Y.230, G.231, Y.232, P.260, W.350 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.229, A:G.231, A:Y.232 EDO.10: 5 residues within 4Å: Chain A: G.220, W.221, K.224, S.342 Chain B: P.119 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.224, A:S.342 Water bridges: A:A.204 EDO.11: 7 residues within 4Å: Chain A: H.21, N.78, K.79, Q.279, S.297, G.298 Chain B: E.280 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.280, A:V.278 EDO.12: 7 residues within 4Å: Chain A: N.248, P.271, G.326, S.327, D.328, G.329 Ligands: NAG.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.248, A:S.327, A:D.328, A:D.328 EDO.13: 4 residues within 4Å: Chain A: S.81, S.99, Q.117 Chain B: H.201 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.99, A:S.99 Water bridges: A:Q.117 EDO.19: 6 residues within 4Å: Chain B: Y.72, P.107, R.108, Q.243, A.244, Q.245 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.108, B:R.108, B:Q.245 EDO.20: 4 residues within 4Å: Chain B: S.228, G.231, Y.232, W.350 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.231, B:G.231, B:W.350 EDO.21: 9 residues within 4Å: Chain B: Y.230, Y.232, Q.233, M.256, S.257, T.258, T.259, Y.312, S.313 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.232, B:S.257, B:T.259, B:S.313 Water bridges: B:T.259 EDO.22: 6 residues within 4Å: Chain B: Y.35, G.62, V.63, L.135, F.136, L.139 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.35, B:G.62 Water bridges: B:L.64 EDO.23: 5 residues within 4Å: Chain B: H.24, N.142, A.143, T.144 Ligands: NAG.16 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.142, B:T.144, B:T.144

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.14: 7 residues within 4Å: Chain A: Q.83, R.186, T.187, D.188, T.189 Chain B: V.190, N.191 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.189

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fusetti, F. et al., Crystal structure of the copper-containing quercetin 2,3-dioxygenase from Aspergillus japonicus. Structure (2002)

Release Date

2002-05-22

Peptides

quercetin 2,3-dioxygenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

quercetin 2,3-dioxygenase

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