SMTL ID : 4kr7.1

Crystal structure of a 4-thiouridine synthetase - RNA complex with bound ATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.42 Å

Oligo State

homo-dimer

Ligands

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 19 residues within 4Å: Chain A: L.180, L.181, S.182, G.184, I.185, D.186, S.187, V.204, T.205, F.206, R.264, M.267, T.285, G.286, E.287, N.288, Q.291, Q.295 Ligands: MG.2 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:S.182, A:S.182, A:I.185, A:D.186, A:D.186, A:S.187, A:S.187, A:S.187, A:T.205, A:F.206, A:F.206, A:G.286, A:G.286, A:Q.291, A:Q.295 Salt bridges: A:R.264 ATP.3: 18 residues within 4Å: Chain B: L.180, L.181, S.182, I.185, D.186, S.187, V.204, T.205, F.206, R.264, M.267, T.285, G.286, E.287, N.288, Q.295, K.320 Ligands: MG.4 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:S.182, B:S.182, B:I.185, B:D.186, B:D.186, B:S.187, B:S.187, B:F.206, B:F.206, B:G.286, B:G.286, B:Q.295 Salt bridges: B:R.264, B:K.320, B:K.320

2 x MG: MAGNESIUM ION(Non-functional Binders)

MG.2: 1 residues within 4Å: Ligands: ATP.1 No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Ligands: ATP.3 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Neumann, P. et al., Crystal structure of a 4-thiouridine synthetase-RNA complex reveals specificity of tRNA U8 modification. Nucleic Acids Res. (2014)

Release Date

2014-04-23

Peptides

Probable tRNA sulfurtransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Probable tRNA sulfurtransferase

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