SMTL ID : 7mjy.1

MiaB in the complex with s-adenosyl-L-homocysteine and RNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

monomer

Ligands

3 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.1: 3 residues within 4Å: Chain A: K.294, D.296, W.299 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.294 Water bridges: A:W.299 PGE.2: 4 residues within 4Å: Chain A: V.31, S.162, F.164, R.418 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.418 PGE.3: 10 residues within 4Å: Chain A: H.275, S.317, D.345, S.346, S.388, Q.421, N.422, R.423, S.447 Chain B: U.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.275, A:S.346, A:S.388, A:N.422 Water bridges: A:V.424

7 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 4 residues within 4Å: Chain A: E.100, K.103, V.140 Ligands: PEG.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.100, A:K.103 Water bridges: A:L.142 PEG.5: 5 residues within 4Å: Chain A: E.100, K.103, Y.182, G.357 Ligands: PEG.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.103, A:K.103 PEG.6: 3 residues within 4Å: Chain A: L.142, T.144, P.181 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.181, A:R.186 PEG.7: 6 residues within 4Å: Chain A: L.122, T.145, E.146, T.147, Y.148, R.149 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.147, A:Y.148, A:R.149 Water bridges: A:D.150 PEG.8: 2 residues within 4Å: Chain A: D.302, R.303 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.303 Water bridges: A:D.260 PEG.9: 4 residues within 4Å: Chain A: Q.333, L.336, E.340 Ligands: PEG.10 No protein-ligand interaction detected (PLIP) PEG.10: 3 residues within 4Å: Chain A: E.379, R.386 Ligands: PEG.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.386

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

F3S.11: 9 residues within 4Å: Chain A: C.27, N.30, T.62, C.63, S.64, I.65, C.97, R.184, Q.215 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)

SF4.12: 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: SAH.13 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:C.171, A:C.175, A:C.178, SAH.13

1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.13: 16 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 Ligands: SF4.12 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:R.66, A:Q.215, A:Q.281, A:Q.281, A:D.319, A:S.353, A:S.353 Water bridges: A:R.66, A:T.252, A:R.293, A:R.293, A:D.319 Salt bridges: A:R.293 pi-Stacking: A:F.321

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.14: 5 residues within 4Å: Chain A: M.29, R.169, G.170, R.184, Q.215 Ligand excluded by 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

Related Entries With Identical Sequence