SMTL ID : 7mjx.2 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.1: 5 residues within 4Å: Chain A: L.122, E.146, Y.148, R.149, D.150 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.148, A:R.149, A:D.150 Water bridges: A:E.146, A:T.147, A:Y.148, A:D.150

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

F3S.2: 10 residues within 4Å: Chain A: C.27, N.30, T.62, C.63, S.64, I.65, C.97, 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 SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.3: 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.5 4 PLIP interactions: 1 Ligand-Ligand interactions, 3 interactions with chain A Metal complexes: MET.5, A:C.171, A:C.175, A:C.178

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

5AD.4: 15 residues within 4Å: Chain A: I.65, R.66, Y.177, P.279, Q.281, D.319, F.321, F.350, K.351, Y.352, S.353, R.355 Chain B: A.7, X.9 Ligands: MET.5 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.66, A:Q.281, A:Q.281, A:S.353, A:S.353 Water bridges: A:R.66 pi-Stacking: A:F.321

1 x MET: METHIONINE(Non-covalent)

MET.5: 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: SF4.3, 5AD.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:T.252, A:P.279 Hydrogen bonds: A:N.216, A:S.253, A:Q.281 Salt bridges: A:H.254, A:R.293

1 x NA: SODIUM ION(Non-functional Binders)

NA.6: 4 residues within 4Å: Chain A: I.266, M.269, P.270, V.272 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.266, A:V.272

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
B

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

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