SMTL ID : 6xi9.1 (1 other biounit)

X-ray crystal structure of MqnE from Pedobacter heparinus in complex with aminofutalosine and methionine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

monomer

Ligands

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

SF4.1: 7 residues within 4Å: Chain A: C.102, Y.104, C.106, F.108, C.109, K.229 Ligands: MET.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Salt bridges: A:E.215 Metal complexes: A:C.102, A:C.106, A:C.109, MET.2

1 x MET: METHIONINE(Non-covalent)

MET.2: 10 residues within 4Å: Chain A: T.147, G.148, V.150, T.179, V.181, G.212, G.213, K.229 Ligands: SF4.1, V47.3 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.179 Hydrogen bonds: A:T.179, A:T.179 Salt bridges: A:K.229

1 x V47: 9-[7-(3-carboxyphenyl)-5,6-dideoxy-beta-D-ribo-heptodialdo-1,4-furanosyl]-9H-purin-6-amine(Non-covalent)

V47.3: 22 residues within 4Å: Chain A: F.108, H.145, K.176, P.210, G.211, G.212, G.213, E.215, N.250, T.252, L.254, I.285, L.287, K.288, F.289, R.290, N.294, K.325, Y.327, D.348 Ligands: MET.2, CL.4 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:I.285 Hydrogen bonds: A:G.211, A:G.213, A:N.250, A:R.290, A:R.290, A:N.294 Water bridges: A:S.110, A:A.214 Salt bridges: A:H.145, A:K.176, A:K.325 pi-Stacking: A:F.108, A:Y.327 pi-Cation interactions: A:H.145

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

CL.4: 6 residues within 4Å: Chain A: H.145, T.147, T.179, P.210, G.212 Ligands: V47.3 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Carl, A.G. et al., Narrow-Spectrum Antibiotic Targeting of the Radical SAM Enzyme MqnE in Menaquinone Biosynthesis. Biochemistry (2020)

Release Date

2020-07-15

Peptides

Aminodeoxyfutalosine synthase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Aminodeoxyfutalosine synthase

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