SMTL ID : 5why.2 (1 other biounit)

Structural Insights into Thioether Bond Formation in the Biosynthesis of Sactipeptides

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.69 Å

Oligo State

monomer

Ligands

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

SF4.1: 6 residues within 4Å: Chain A: C.347, S.349, C.365, C.416, A.417, A.418 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.347, A:C.365, A:C.416 SF4.2: 7 residues within 4Å: Chain A: C.107, L.109, C.111, C.114, G.157, R.225 Ligands: SAM.4 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.107, A:C.111, A:C.114 SF4.3: 8 residues within 4Å: Chain A: E.402, C.403, C.406, C.412, G.415, V.430, C.435, K.439 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.403, A:C.406, A:C.412, A:C.435

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

SAM.4: 17 residues within 4Å: Chain A: Y.113, C.114, F.155, G.156, G.157, E.158, T.189, T.190, N.191, S.213, R.225, R.256, T.258, P.285, V.286, V.287 Ligands: SF4.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:T.189 Hydrogen bonds: A:Y.113, A:G.157, A:N.191, A:S.213, A:S.213, A:R.225, A:R.256, A:V.287, A:V.287, A:Q.367 Salt bridges: A:R.225 pi-Stacking: A:Y.113, A:Y.113

4 x CA: CALCIUM ION(Non-covalent)

CA.5: 2 residues within 4Å: Chain A: G.14, D.31 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.31 CA.6: 2 residues within 4Å: Chain A: D.106, R.110 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.106, A:D.106 CA.7: 1 residues within 4Å: Chain A: N.183 No protein-ligand interaction detected (PLIP) CA.8: 1 residues within 4Å: Chain A: E.309 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.309

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Radical SAM domain protein

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