SMTL ID : 7mjw.1 (1 other biounit)

Methylated MiaB in the complex with 5'-deoxyadenosine, methionine and RNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

1 x ZKP: FE3-S4 methylated cluster(Non-covalent)

ZKP.1: 11 residues within 4Å: Chain A: C.27, N.30, T.62, C.63, S.64, I.65, C.97, V.180, R.184, Q.215 Chain B: X.9 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.27, A:C.63, A:C.97

1 x MET: METHIONINE(Non-covalent)

MET.2: 11 residues within 4Å: Chain A: Q.215, N.216, T.252, S.253, H.254, P.255, P.279, Q.281, R.293 Ligands: 5AD.3, SF4.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.252, A:P.279 Hydrogen bonds: A:N.216, A:Q.281 Salt bridges: A:H.254, A:R.293

1 x 5AD: 5'-DEOXYADENOSINE(Non-covalent)

5AD.3: 14 residues within 4Å: Chain A: I.65, R.66, Y.177, Q.281, D.319, F.321, F.350, K.351, Y.352, S.353, R.355 Chain B: A.7, X.9 Ligands: MET.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.66, A:Q.281, A:Q.281, A:D.319, A:S.353, A:S.353 Water bridges: A:R.66 pi-Stacking: A:F.321

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.4: 12 residues within 4Å: Chain A: C.171, N.173, F.174, C.175, Y.177, C.178, V.180, P.181, N.216, H.254, R.293 Ligands: MET.2 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.171, A:C.175, A:C.178

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain A: I.266, M.269, P.270, V.272 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:I.266, A:M.269, A:V.272, H2O.3, H2O.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Esakova, O.A. et al., Structural basis for tRNA methylthiolation by the radical SAM enzyme MiaB. Nature (2021)

Release Date

2021-09-15

Peptides

tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase

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