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

Crystal Structure of Quercetin 2,3-dioxygenase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]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-MAN-MAN-MAN.1: 11 residues within 4Å: Chain A: V.190, N.191 Chain B: L.61, Q.83, W.85, T.184, R.186, T.187, D.188, T.189 Ligands: EDO.28 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.85 Hydrogen bonds: B:T.189, B:T.189

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-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.2: 7 residues within 4Å: Chain A: Q.83, T.184, T.187, D.188, T.189 Chain B: V.190, N.191 1 PLIP interactions: 1 interactions with chain A Water bridges: A:P.185, A:P.185 Hydrogen bonds: A:T.189

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

NAG.3: 3 residues within 4Å: Chain A: Q.69, R.108, N.109 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.109 Water bridges: A:Q.69, A:Q.69, A:Q.69 NAG.4: 4 residues within 4Å: Chain A: N.248, G.272, S.325, G.326 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.248 Water bridges: A:N.248, A:P.271, A:A.273, A:S.325, A:S.325 NAG.5: 3 residues within 4Å: Chain A: N.142, A.143, T.144 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.142, A:T.144 Water bridges: A:T.144 NAG.6: 1 residues within 4Å: Chain A: N.90 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.90 NAG.17: 2 residues within 4Å: Chain B: R.108, N.109 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.109 Water bridges: B:Q.69 NAG.18: 4 residues within 4Å: Chain B: N.248, G.272, S.325, G.326 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.248 Water bridges: B:P.271, B:A.273, B:S.325, B:S.325, B:S.327 NAG.19: 4 residues within 4Å: Chain B: R.26, Y.137, N.142 Ligands: EDO.30 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.26, B:N.142

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

CU.7: 5 residues within 4Å: Chain A: H.66, H.68, E.73, H.112 Ligands: EDO.10 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.66, A:H.68, A:H.112, H2O.12 CU.20: 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.29

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

EDO.8: 7 residues within 4Å: Chain A: Y.72, P.107, R.108, A.211, Q.243, A.244, Q.245 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: P.223, K.224, Y.225, E.340, W.341 Ligand excluded by PLIP EDO.10: 9 residues within 4Å: Chain A: V.63, H.66, H.68, F.132, L.135, F.136, V.177 Ligands: CU.7, EDO.16 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: S.228, G.231, Y.232, W.350 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: W.341, S.342, S.343 Chain B: S.154 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: L.226, S.228, E.339, W.341, P.347 Ligands: EDO.15 Ligand excluded by PLIP EDO.14: 1 residues within 4Å: Chain A: D.349 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain A: Y.232, P.347, D.349, W.350 Ligands: EDO.13 Ligand excluded by PLIP EDO.16: 8 residues within 4Å: Chain A: Y.35, T.53, E.73, F.75, F.114, M.123, F.136 Ligands: EDO.10 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain B: Y.72, P.107, R.108, Q.243, A.244, Q.245 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain B: T.92, R.186, P.195 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain B: Q.286, G.288, E.308, F.309, K.310 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain B: S.228, G.231, Y.232, W.350 Ligand excluded by PLIP EDO.25: 8 residues within 4Å: Chain A: E.280 Chain B: H.21, N.78, E.122, V.278, Q.279, S.297, G.298 Ligand excluded by PLIP EDO.26: 8 residues within 4Å: Chain A: G.281, R.282, G.296, S.297 Chain B: G.281, R.282, G.296, S.297 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain B: S.228, Y.232, E.339 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain B: P.185, R.186, T.187 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN-MAN-MAN.1 Ligand excluded by PLIP EDO.29: 9 residues within 4Å: Chain B: Y.230, Y.232, Q.233, M.256, S.257, T.258, T.259, Y.312, S.313 Ligand excluded by PLIP EDO.30: 3 residues within 4Å: Chain B: H.24, R.26 Ligands: NAG.19 Ligand excluded by PLIP

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
A

B
C

quercetin 2,3-dioxygenase

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