SMTL ID : 6ei9.2 (1 other biounit)

Crystal structure of E. coli tRNA-dihydrouridine synthase B (DusB)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

monomer

Ligands

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 20 residues within 4Å: Chain A: A.34, P.35, M.36, A.37, I.39, Q.89, N.116, C.119, K.158, H.188, F.196, N.219, G.220, D.221, M.241, I.242, G.243, R.244 Ligands: SO4.3, SO4.6 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:M.36, A:I.39, A:F.196, A:R.244 Hydrogen bonds: A:A.37, A:Q.89, A:Q.89, A:K.158, A:N.219, A:G.220, A:D.221, A:D.221, A:D.221, A:G.243, A:R.244, A:R.244 Water bridges: A:I.222, A:A.245 Salt bridges: A:R.244

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: R.28, Y.49, E.50, G.52 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.28, A:R.28 Water bridges: A:N.29, A:E.50

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 7 residues within 4Å: Chain A: G.118, C.119, P.120, K.158, R.160, H.188 Ligands: FMN.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.118 Salt bridges: A:K.158, A:R.160, A:H.188 SO4.4: 4 residues within 4Å: Chain A: P.165, E.166, H.167, R.168 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.165, A:R.168 Salt bridges: A:R.168 SO4.5: 4 residues within 4Å: Chain A: N.29, R.30, Q.257, D.261 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.30, A:Q.257, A:D.261 Water bridges: A:G.18, A:R.30 SO4.6: 4 residues within 4Å: Chain A: A.37, C.119, K.122 Ligands: FMN.1 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.122

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.7: 7 residues within 4Å: Chain A: R.42, D.81, E.82, R.86, E.107, S.108, G.109 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bou-Nader, C. et al., Unveiling structural and functional divergences of bacterial tRNA dihydrouridine synthases: perspectives on the evolution scenario. Nucleic Acids Res. (2018)

Release Date

2018-01-17

Peptides

tRNA-dihydrouridine synthase B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

tRNA-dihydrouridine synthase B

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