SMTL ID : 7mjv.1

MiaB in the complex with s-adenosylmethionine and RNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.24 Å

Oligo State

monomer

Ligands

1 x F3S: FE3-S4 CLUSTER(Non-covalent)

F3S.1: 10 residues within 4Å: Chain A: C.27, N.30, T.62, C.63, S.64, I.65, C.97, R.184, Q.215 Ligands: SAM.3 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.27, A:C.63, A:C.97

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

SF4.2: 12 residues within 4Å: Chain A: C.171, N.173, F.174, C.175, Y.177, C.178, V.180, P.181, Q.215, H.254, R.293 Ligands: SAM.3 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.171, A:C.175, A:C.178

1 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.3: 18 residues within 4Å: Chain A: I.65, R.66, Y.177, Q.215, T.252, P.279, Q.281, R.293, D.319, F.321, F.350, K.351, Y.352, S.353, R.355 Chain B: X.11 Ligands: F3S.1, SF4.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.66, A:Q.215, A:Q.281, A:Q.281, A:S.353, A:S.353 Salt bridges: A:R.293 pi-Stacking: A:F.321

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: I.266, M.269, P.270, V.272, E.420 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:I.266, A:M.269, A:V.272, H2O.1 MG.5: 4 residues within 4Å: Chain A: R.66, F.350, K.351 Chain B: A.12 No protein-ligand interaction detected (PLIP)

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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