SMTL ID : 4wq5.2 (1 other biounit)

YgjD(V85E)-YeaZ heterodimer in complex with ATP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.33 Å

Oligo State

hetero-oligomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: C.10, D.11, E.12, D.300 Ligands: ATP.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.11, A:D.300, H2O.1

1 x FE: FE (III) ION(Non-covalent)

FE.2: 5 residues within 4Å: Chain A: H.111, M.112, H.115, D.300 Ligands: ATP.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.111, A:H.115, A:D.300

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

ATP.3: 22 residues within 4Å: Chain A: H.111, M.112, H.115, S.136, G.137, G.138, H.139, G.163, F.166, D.167, G.180, P.181, G.267, G.268, V.269, A.271, N.272, C.298, T.299, D.300 Ligands: MG.1, FE.2 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:S.136, A:G.137, A:G.138, A:H.139, A:D.167, A:G.180, A:G.268, A:A.271, A:N.272, A:D.300 Water bridges: A:R.273 Salt bridges: A:H.115, A:H.115, A:H.139 pi-Stacking: A:F.166

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 3 residues within 4Å: Chain A: Y.30, R.53, K.54 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.30 Salt bridges: A:R.53, A:K.54 ACT.5: 4 residues within 4Å: Chain B: R.32, E.33, H.34, T.35 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:H.34 Hydrogen bonds: B:T.35

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain B: S.67, F.68, T.69, R.118 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.68, B:T.69, B:T.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, W. et al., The ATP-mediated formation of the YgjD-YeaZ-YjeE complex is required for the biosynthesis of tRNA t6A in Escherichia coli. Nucleic Acids Res. (2015)

Release Date

2015-01-28

Peptides

tRNA N6-adenosine threonylcarbamoyltransferase: A
tRNA threonylcarbamoyladenosine biosynthesis protein TsaB: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

tRNA N6-adenosine threonylcarbamoyltransferase

tRNA threonylcarbamoyladenosine biosynthesis protein TsaB

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