SMTL ID : 4wfs.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.68 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, M.240 Ligands: SO4.3 20 PLIP interactions: 20 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:N.107, A:K.149, A:K.149, A:N.208, A:G.209, A:G.210, A:S.211, A:S.211, A:A.236, A:R.237 Water bridges: A:M.234, A:R.237 Salt bridges: A:R.237

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

SO4.2: 4 residues within 4Å: Chain A: G.309, L.310, G.311, A.312 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.311, A:A.312 SO4.3: 5 residues within 4Å: Chain A: G.109, K.149, R.151, H.177 Ligands: FMN.1 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:K.149, A:R.151, A:H.177 SO4.4: 3 residues within 4Å: Chain A: R.15, T.273, N.274 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.274, A:N.274 Salt bridges: A:R.15 SO4.5: 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

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

CL.6: 1 residues within 4Å: Chain A: R.252 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bou-Nader, C. et al., An extended dsRBD is required for post-transcriptional modification in human tRNAs. Nucleic Acids Res. (2015)

Release Date

2015-10-07

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