SMTL ID : 8hfb.1

Evolved variant of quercetin 2,4-dioxygenase from Bacillus subtilis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.24 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 2 residues within 4Å: Chain A: P.60, N.149 No protein-ligand interaction detected (PLIP) EDO.2: 5 residues within 4Å: Chain A: H.236, E.237, Y.238, F.295, L.332 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.237, A:Y.238 EDO.3: 5 residues within 4Å: Chain A: L.74, R.113, Y.244, L.246, G.264 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Water bridges: B:E.247 Hydrogen bonds: A:R.113, A:R.113, A:Y.244, A:Y.244 EDO.7: 5 residues within 4Å: Chain B: R.113, Y.244, C.245, L.246, G.264 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.113, B:R.113, B:Y.244, B:Y.244

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: D.44, G.121, N.122 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.122

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

NI.5: 4 residues within 4Å: Chain A: H.234, H.236, E.241, H.275 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.234, A:H.236, A:E.241, A:H.275, H2O.3, H2O.3 NI.6: 4 residues within 4Å: Chain A: H.62, H.64, E.69, H.103 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.62, A:H.64, A:E.69, A:H.103, H2O.3 NI.8: 4 residues within 4Å: Chain B: H.62, H.64, E.69, H.103 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.62, B:H.64, B:E.69, B:H.103, H2O.5 NI.9: 4 residues within 4Å: Chain B: H.234, H.236, E.241, H.275 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.234, B:H.236, B:E.241, B:H.275, H2O.5, H2O.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Eom, H. et al., Underlying Role of Hydrophobic Environments in Tuning Metal Elements for Efficient Enzyme Catalysis. J.Am.Chem.Soc. (2023)

Release Date

2023-03-08

Peptides

Quercetin 2,3-dioxygenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Quercetin 2,3-dioxygenase