SMTL ID : 5wgg.1

Structural Insights into Thioether Bond Formation in the Biosynthesis of Sactipeptides

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

hetero-1-1-mer

Ligands

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

SF4.1: 8 residues within 4Å: Chain A: C.347, S.349, C.365, Q.367, C.416, A.417, A.418 Chain B: C.21 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A, Metal complexes: B:C.21, A:C.347, A:C.365, A:C.416 SF4.2: 10 residues within 4Å: Chain A: C.107, L.109, C.111, C.114, A.116, G.156, G.157, N.191, R.225 Ligands: SAM.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:C.107, A:C.111, A:C.114, SAM.4 SF4.3: 7 residues within 4Å: Chain A: C.403, C.406, K.409, C.412, G.414, G.415, C.435 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.403, A:C.406, A:C.412, A:C.435, H2O.5

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

SAM.4: 19 residues within 4Å: Chain A: Y.113, C.114, F.115, F.155, G.156, G.157, E.158, P.159, T.189, T.190, N.191, S.213, R.225, R.256, T.258, V.286, V.287, Q.367 Ligands: SF4.2 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:T.189 Hydrogen bonds: A:Y.113, A:G.157, A:T.189, A:N.191, A:S.213, A:S.213, A:R.225, A:R.256, A:R.256, A:T.258, A:V.287, A:V.287, A:Q.367 Water bridges: A:I.214 Salt bridges: A:R.225 pi-Stacking: A:Y.113 pi-Cation interactions: A:H.366

2 x CA: CALCIUM ION(Non-covalent)

CA.5: 1 residues within 4Å: Chain A: D.31 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.31, A:D.31, H2O.2, H2O.5, H2O.5 CA.6: 1 residues within 4Å: Chain A: S.11 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.11, H2O.1, H2O.3, H2O.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grove, T.L. et al., Structural Insights into Thioether Bond Formation in the Biosynthesis of Sactipeptides. J. Am. Chem. Soc. (2017)

Release Date

2017-07-26

Peptides

Radical SAM domain protein: A
CteA: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Radical SAM domain protein

CteA

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