SMTL ID : 6efn.1

Structure of a RiPP maturase, SkfB

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.29 Å

Oligo State

homo-dimer

Ligands

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

SAM.1: 18 residues within 4Å: Chain A: F.125, C.126, Y.127, T.161, G.163, E.164, F.188, S.189, N.190, S.213, R.225, A.251, T.253, K.281, T.282, L.283, A.288 Ligands: SF4.2 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.188 Hydrogen bonds: A:Y.127, A:E.164, A:S.189, A:N.190, A:S.213, A:S.213, A:S.213, A:R.225, A:T.253, A:L.283, A:L.283 Water bridges: A:Q.354 Salt bridges: A:R.225 pi-Stacking: A:Y.127 pi-Cation interactions: A:F.188 SAM.5: 18 residues within 4Å: Chain B: F.125, C.126, Y.127, T.161, G.163, E.164, F.188, S.189, N.190, S.213, R.225, A.251, T.253, K.281, T.282, L.283, A.288 Ligands: SF4.6 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:F.188 Hydrogen bonds: B:Y.127, B:E.164, B:E.164, B:S.189, B:N.190, B:S.213, B:S.213, B:S.213, B:R.225, B:T.253, B:L.283, B:L.283 Water bridges: B:Q.354 Salt bridges: B:R.225 pi-Stacking: B:Y.127 pi-Cation interactions: B:F.188

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

SF4.2: 11 residues within 4Å: Chain A: C.119, L.121, S.122, C.123, C.126, S.130, G.163, N.190, R.225, R.287 Ligands: SAM.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:C.119, A:C.123, A:C.126, SAM.1 SF4.6: 11 residues within 4Å: Chain B: C.119, L.121, S.122, C.123, C.126, S.130, G.163, N.190, R.225, R.287 Ligands: SAM.5 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:C.119, B:C.123, B:C.126, SAM.5

2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.3: 6 residues within 4Å: Chain A: P.337, C.353, L.355, C.387, K.388, C.389 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.353, A:C.387, A:C.389, H2O.15 FES.7: 6 residues within 4Å: Chain B: P.337, C.353, L.355, C.387, K.388, C.389 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.353, B:C.387, B:C.389, H2O.30

2 x MG: MAGNESIUM ION(Non-functional Binders)

MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grell, T.A.J. et al., Structure of a RiPP maturase, SkfB. J.Biol.Chem. (2018)

Release Date

2018-10-24

Peptides

Sporulation killing factor maturation protein SkfB: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Sporulation killing factor maturation protein SkfB