SMTL ID : 6xig.1

X-ray crystal structure of MqnE from Pedobacter heparinus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

homo-dimer

Ligands

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

SF4.1: 11 residues within 4Å: Chain A: C.102, Y.104, C.106, F.108, C.109, S.112, G.148, G.149, V.181, K.229 Ligands: TAR.2 4 PLIP interactions: 4 interactions with chain A, Salt bridges: A:E.215 Metal complexes: A:C.102, A:C.106, A:C.109 SF4.4: 11 residues within 4Å: Chain B: C.102, Y.104, C.106, F.108, C.109, S.112, G.148, G.149, V.181, K.229 Ligands: TAR.6 4 PLIP interactions: 4 interactions with chain B, Salt bridges: B:E.215 Metal complexes: B:C.102, B:C.106, B:C.109

5 x TAR: D(-)-TARTARIC ACID(Non-covalent)

TAR.2: 8 residues within 4Å: Chain A: T.147, G.148, T.179, V.181, G.212, G.213, K.229 Ligands: SF4.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.148 Salt bridges: A:K.229, A:K.229 TAR.3: 5 residues within 4Å: Chain A: M.130, K.134, R.165, A.168, H.169 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.165 Salt bridges: A:K.134, A:R.165, A:H.169 TAR.5: 5 residues within 4Å: Chain B: H.95, E.97, V.132, K.135, Y.136 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:H.95, B:E.97, B:Y.136, B:Y.136 Water bridges: B:H.95, B:H.95, B:Y.136, B:Y.136 Salt bridges: B:H.95, B:K.135 TAR.6: 8 residues within 4Å: Chain B: T.147, G.148, T.179, V.181, G.212, G.213, K.229 Ligands: SF4.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.148 Salt bridges: B:K.229 TAR.7: 4 residues within 4Å: Chain B: M.130, K.134, R.165, H.169 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.134, B:H.169 Water bridges: B:D.127, B:R.165 Salt bridges: B:K.134, B:R.165

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Aminodeoxyfutalosine synthase

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