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

Crystal structure of E. coli YgjD-YeaZ heterodimer in complex with ADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.33 Å

Oligo State

hetero-1-1-mer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 20 residues within 4Å: Chain A: H.111, M.112, H.115, S.136, G.137, G.138, G.163, F.166, D.167, G.180, P.181, G.268, V.269, A.271, N.272, C.298, T.299, D.300 Ligands: MG.2, FE.3 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:G.137, A:G.138, A:D.167, A:G.180, A:G.268, A:N.272, A:D.300 Water bridges: A:S.184, A:R.273, A:R.273, A:D.300 Salt bridges: A:H.111, A:H.115 pi-Stacking: A:F.166 ADP.6: 13 residues within 4Å: Chain A: V.85, V.325 Chain B: C.30, P.31, R.32, E.33, H.34, T.35, S.67, T.69, I.73, R.118 Ligands: ACT.9 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:C.30, B:R.32, B:H.34, B:T.35, B:S.67 Water bridges: B:S.67, B:F.68, B:T.69, B:T.69, A:V.325, A:V.325 Salt bridges: B:R.118

1 x MG: MAGNESIUM ION(Non-covalent)

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

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

FE.3: 4 residues within 4Å: Chain A: H.111, H.115, D.300 Ligands: ADP.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.111, A:H.115, A:D.300

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

ACT.4: 4 residues within 4Å: Chain A: P.205, G.206, R.253 Ligands: ACT.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.205 Water bridges: A:R.253 Salt bridges: A:R.253 ACT.5: 6 residues within 4Å: Chain A: T.202, D.203, R.204, P.205, R.253 Ligands: ACT.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.203 Water bridges: A:R.253, A:R.253, A:R.253 Salt bridges: A:R.253 ACT.7: 5 residues within 4Å: Chain B: V.143, L.218, R.219, N.220, N.221 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:N.220 Hydrogen bonds: B:N.220, B:N.221 Water bridges: B:V.143, B:V.143, B:N.221, B:N.221 ACT.8: 5 residues within 4Å: Chain B: A.108, T.109, R.110, E.159, V.161 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.108, B:V.161 Hydrogen bonds: B:T.109, B:T.109, B:R.110, B:E.159 ACT.9: 2 residues within 4Å: Chain B: R.32 Ligands: ADP.6 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.32 ACT.10: 6 residues within 4Å: Chain B: G.66, S.67, F.68, A.117, Y.123, R.219 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.68 Hydrogen bonds: B:G.66 Water bridges: B:R.219 Salt bridges: B:R.219 ACT.11: 7 residues within 4Å: Chain A: V.52, R.53, V.56, P.57 Chain B: Q.79, E.211, A.213 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.56, A:P.57 Hydrogen bonds: B:Q.79, B:A.213

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

2015-03-04

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

tRNA N6-adenosine threonylcarbamoyltransferase

tRNA threonylcarbamoyladenosine biosynthesis protein TsaB

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