SMTL ID : 7mjz.1

The structure of MiaB with pentasulfide bridge

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.08 Å

Oligo State

monomer

Ligands

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

SF4.1: 10 residues within 4Å: Chain A: G.26, C.27, N.30, C.63, S.64, I.65, C.97, V.180, R.184 Ligands: PS5.3 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.27, A:C.63, A:C.97 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: PS5.3 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.171, A:C.175, A:C.178

1 x PS5: PENTASULFIDE-SULFUR(Non-covalent)

PS5.3: 4 residues within 4Å: Chain A: V.180, Q.215 Ligands: SF4.1, SF4.2 No protein-ligand interaction detected (PLIP)

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

NA.4: 4 residues within 4Å: Chain A: I.266, M.269, P.270, V.272 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.270

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