SMTL ID : 6gri.1

E. coli Microcin synthetase McbBCD complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-4-2-2-mer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.192, C.195, C.290, C.292 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.192, A:C.195, A:C.290, A:C.292 ZN.4: 4 residues within 4Å: Chain B: C.192, C.195, C.290, C.292 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.192, B:C.195, B:C.290, B:C.292 ZN.9: 4 residues within 4Å: Chain E: C.192, C.195, C.290, C.292 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.192, E:C.195, E:C.290, E:C.292 ZN.12: 4 residues within 4Å: Chain F: C.192, C.195, C.290, C.292 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.192, F:C.195, F:C.290, F:C.292

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 3 residues within 4Å: Chain A: R.199, R.203, R.210 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.199, A:R.203 SO4.6: 5 residues within 4Å: Chain C: G.123, G.124, K.201, Y.202 Ligands: FMN.5 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.124, C:Y.202, C:Y.202 Salt bridges: C:K.201 SO4.10: 3 residues within 4Å: Chain E: R.199, R.203, R.210 2 PLIP interactions: 2 interactions with chain E Salt bridges: E:R.199, E:R.203 SO4.14: 5 residues within 4Å: Chain G: G.123, G.124, K.201, Y.202 Ligands: FMN.13 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:G.124, G:Y.202, G:Y.202 Salt bridges: G:K.201

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

CL.3: 2 residues within 4Å: Chain A: R.155, K.159 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain C: F.43, V.44, S.45 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain D: A.248, N.249, S.250, K.253 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain E: R.155, K.159 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain G: F.43, V.44, S.45 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain H: A.248, N.249, S.250, K.253 Ligand excluded by PLIP

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.5: 18 residues within 4Å: Chain C: R.117, P.121, S.122, G.123, A.125, M.209 Chain G: R.82, P.84, S.85, R.181, Y.218, R.233, V.234, W.235, A.236, G.237, I.258 Ligands: SO4.6 14 PLIP interactions: 4 interactions with chain C, 10 interactions with chain G Hydrogen bonds: C:S.122, C:G.124, C:A.125, G:S.85, G:S.85, G:R.181, G:R.181, G:R.233, G:A.236, G:G.237 Salt bridges: C:R.117, G:R.82 Hydrophobic interactions: G:V.234, G:A.236 FMN.13: 18 residues within 4Å: Chain C: R.82, P.84, S.85, R.181, Y.218, R.233, V.234, W.235, A.236, G.237, I.258 Chain G: R.117, P.121, S.122, G.123, A.125, M.209 Ligands: SO4.14 14 PLIP interactions: 4 interactions with chain G, 10 interactions with chain C Hydrogen bonds: G:S.122, G:G.124, G:A.125, C:S.85, C:S.85, C:R.181, C:R.181, C:R.233, C:A.236, C:G.237 Salt bridges: G:R.117, C:R.82 Hydrophobic interactions: C:V.234, C:A.236

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ghilarov, D. et al., Architecture of Microcin B17 Synthetase: An Octameric Protein Complex Converting a Ribosomally Synthesized Peptide into a DNA Gyrase Poison. Mol. Cell (2019)

Release Date

2019-01-30

Peptides

Microcin B17-processing protein McbB: ABEF
Microcin B17-processing protein McbC: CG
Microcin B17-processing protein McbD: DH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

B
2

E
1

F
2

C
C

G
C

D
D

H
D

Microcin B17-processing protein McbB

Microcin B17-processing protein McbC

Microcin B17-processing protein McbD

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