SMTL ID : 6ezc.1

Crystal Structure of human tRNA-dihydrouridine(20) synthase catalytic domain E294K Q305K double mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 20 residues within 4Å: Chain A: A.11, P.12, M.13, V.14, V.16, E.37, Q.81, N.107, K.149, H.177, N.208, G.209, G.210, S.211, V.235, A.236, R.237, M.240 Ligands: CL.5, GOL.6 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:M.13, A:V.16, A:R.237 Hydrogen bonds: A:P.12, A:V.14, A:E.37, A:Q.81, A:Q.81, A:N.107, 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, A:G.210 Salt bridges: A:R.237

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

SO4.2: 2 residues within 4Å: Chain A: S.85, R.89 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.85 Water bridges: A:R.89 Salt bridges: A:R.89 SO4.3: 5 residues within 4Å: Chain A: R.15, H.271, T.273, N.274 Ligands: PGE.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.274 Water bridges: A:T.273, A:T.273 Salt bridges: A:R.15 SO4.4: 3 residues within 4Å: Chain A: R.73, N.76, R.77 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.76 Salt bridges: A:R.77 SO4.9: 2 residues within 4Å: Chain A: S.300, R.302 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.300 Water bridges: A:S.301 Salt bridges: A:R.302 SO4.10: 1 residues within 4Å: Chain A: R.293 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.293

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 5 residues within 4Å: Chain A: G.109, K.149, R.151, H.177 Ligands: FMN.1 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: E.37, N.107, G.109 Ligands: FMN.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.107 Water bridges: A:R.151 GOL.7: 2 residues within 4Å: Chain A: R.143, R.144 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.143, A:R.144, A:R.144

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.8: 9 residues within 4Å: Chain A: T.18, E.36, V.66, R.69, D.269, N.270, H.271, N.274 Ligands: SO4.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.36, A:H.271, A:N.274 Water bridges: A:R.69, A:R.69

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