SMTL ID : 6ei9.1 (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: 17 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, G.243, R.244 Ligands: GOL.2 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:M.36, A:F.196, A:R.244 Hydrogen bonds: A:P.35, A:A.37, A:Q.89, A:Q.89, A:K.158, A:N.219, A:G.220, A:D.221, A:M.241, A:G.243, A:R.244, A:R.244 Water bridges: A:K.122, A:I.222, A:I.222, A:I.222, A:I.222 Salt bridges: A:R.244

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 10 residues within 4Å: Chain A: N.116, G.118, C.119, P.120, K.158, I.159, R.160, H.188, F.196 Ligands: FMN.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.160, A:R.160, A:H.188

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

SO4.3: 3 residues within 4Å: Chain A: R.168, E.201, D.203 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.201, A:D.203 Water bridges: A:R.168 Salt bridges: A:R.168 SO4.4: 4 residues within 4Å: Chain A: E.59, V.88, N.105, S.108 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.58, A:N.105, A:S.108 SO4.5: 3 residues within 4Å: Chain A: P.16, R.229, L.260 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.16, A:P.16 Salt bridges: A:R.229 SO4.6: 1 residues within 4Å: Chain A: Y.295 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
A

tRNA-dihydrouridine synthase B

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