SMTL ID : 6ezb.1

Crystal Structure of human tRNA-dihydrouridine(20) synthase catalytic domain Q305K mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

monomer

Ligands

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 17 residues within 4Å: Chain A: A.11, P.12, M.13, V.14, E.37, Q.81, N.107, K.149, H.177, N.208, G.209, G.210, S.211, A.236, R.237 Ligands: GOL.5, SO4.6 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:M.13, A:R.237 Hydrogen bonds: A:P.12, A:V.14, A:E.37, A:Q.81, A:Q.81, A:K.149, A:K.149, A:N.208, A:G.209, A:S.211, A:S.211, A:M.234, A:A.236, A:R.237 Water bridges: A:G.210 Salt bridges: A:R.237

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

SO4.2: 4 residues within 4Å: Chain A: R.15, H.271, T.273, N.274 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.274 Salt bridges: A:R.15 SO4.3: 2 residues within 4Å: Chain A: S.85, R.89 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.89 SO4.4: 2 residues within 4Å: Chain A: N.76, R.77 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.76 Salt bridges: A:R.77 SO4.6: 6 residues within 4Å: Chain A: G.109, K.149, R.151, H.177 Ligands: FMN.1, GOL.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.109 Salt bridges: A:K.149, A:R.151, A:H.177

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: V.14, E.37, N.107, C.110, P.111 Ligands: FMN.1, SO4.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.107

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bou-Nader, C. et al., Electrostatic Potential in the tRNA Binding Evolution of Dihydrouridine Synthases. Biochemistry (2018)

Release Date

2018-09-26

Peptides

tRNA-dihydrouridine(20) synthase [NAD(P)+]-like: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

tRNA-dihydrouridine(20) synthase [NAD(P)+]-like