SMTL ID : 5flj.4 (5 other biounits)

enzyme-substrate-dioxygen complex of Ni-quercetinase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

homo-dimer

Ligands

2 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 5 residues within 4Å: Chain A: H.69, H.71, E.76, H.115 Ligands: QUE.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.69, A:H.71, A:E.76, A:H.115, H2O.3 NI.5: 6 residues within 4Å: Chain B: H.69, H.71, E.76, H.115 Ligands: QUE.6, OXY.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.69, B:H.71, B:E.76, B:H.115

2 x QUE: 3,5,7,3',4'-PENTAHYDROXYFLAVONE(Non-covalent)

QUE.2: 21 residues within 4Å: Chain A: L.35, F.36, F.56, C.58, I.66, H.69, H.71, E.76, V.77, F.78, Y.117, V.126, V.127, G.128, V.129, F.137, F.140, F.141, V.174, F.176 Ligands: NI.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.35, A:I.66, A:F.78, A:Y.117, A:F.140, A:F.141 Hydrogen bonds: A:V.77, A:V.127 pi-Stacking: A:F.141 QUE.6: 21 residues within 4Å: Chain B: L.35, F.36, F.56, C.58, I.66, H.69, H.71, E.76, V.77, F.78, Y.117, V.126, V.127, G.128, V.129, F.137, F.140, F.141, F.176 Ligands: NI.5, OXY.7 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.78, B:Y.117, B:F.140, B:F.141 Hydrogen bonds: B:V.77, B:V.77, B:V.127 pi-Stacking: B:F.56, B:F.141

3 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 8 residues within 4Å: Chain A: Y.79, T.81, P.103, G.104 Chain B: K.27, T.81, Q.82, Q.125 No protein-ligand interaction detected (PLIP) DMS.4: 5 residues within 4Å: Chain A: R.12, F.14, L.29, G.30, R.32 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.32, A:R.32 Water bridges: A:F.14, A:R.32 DMS.8: 6 residues within 4Å: Chain A: Q.82, Q.125 Chain B: Y.79, I.80, P.103, G.104 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.79

1 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.7: 6 residues within 4Å: Chain B: H.69, E.76, F.78, H.115 Ligands: NI.5, QUE.6 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jeoung, J. et al., Quercetin 2,4-Dioxygenase Activates Dioxygen in a Side-on O2 -Ni Complex. Angew.Chem.Int.Ed.Engl. (2016)

Release Date

2016-06-01

Peptides

QUERCETINASE QUED: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

QUERCETINASE QUED

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