SMTL ID : 6puq.1

1.56 A crystal structure of flavodoxin-like domain of Schizosaccharomyces japonicus putative tRNAPhe 4-demethylwyosine synthase Tyw1 in complex with FMN

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

monomer

Ligands

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 20 residues within 4Å: Chain A: T.65, L.66, G.67, G.68, S.69, T.70, P.118, S.119, Y.120, A.121, F.158, G.159, D.160, Y.164, L.168, F.169, C.170, Y.171, V.196 Ligands: MG.2 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:Y.120, A:Y.120 Hydrogen bonds: A:L.66, A:G.67, A:G.68, A:S.69, A:S.69, A:S.69, A:T.70, A:T.70, A:S.119, A:S.119, A:Y.120, A:A.121, A:D.160, A:L.168, A:C.170 pi-Stacking: A:Y.164, A:Y.164

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: S.69, T.70, F.73, F.158 Ligands: FMN.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.69, A:T.70 MG.3: 7 residues within 4Å: Chain A: L.117, P.118, S.119, G.157, F.158, C.170, A.173 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:L.117, A:S.119, A:F.158 MG.4: 7 residues within 4Å: Chain A: A.154, V.155, D.177, R.187, A.189, P.190, L.191 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.177, A:A.189 MG.5: 6 residues within 4Å: Chain A: Y.120, I.122, E.123, S.124, D.127, Q.172 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:I.122, A:S.124 MG.6: 4 residues within 4Å: Chain A: S.64, T.65, N.94, D.96 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.64, A:D.96, H2O.3

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 2 residues within 4Å: Chain A: C.57, N.110 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.110

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.8: 3 residues within 4Å: Chain A: Q.86, T.87, E.88 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sjekloca, L. et al., Biochemical and structural characterization of the flavodoxin-like domain of the Schizosaccharomyces japonicus putative tRNAPhe 4-demethylwyosine synthase Tyw1 in complex with FMN. MicroPubl Biol (2022)

Release Date

2020-07-22

Peptides

Wybutosine biosynthesis protein Tyw1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Wybutosine biosynthesis protein Tyw1