SMTL ID : 6gos.1

E. coli Microcin synthetase McbBCD complex with pro-MccB17 bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-2-4-2-2-mer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 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.4: 4 residues within 4Å: Chain C: C.192, C.195, C.290, C.292 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.192, C:C.195, C:C.290, C:C.292 ZN.14: 4 residues within 4Å: Chain G: C.192, C.195, C.290, C.292 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.192, G:C.195, G:C.290, G:C.292 ZN.17: 4 residues within 4Å: Chain H: C.192, C.195, C.290, C.292 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.192, H:C.195, H:C.290, H:C.292

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

SO4.2: 3 residues within 4Å: Chain B: R.199, R.203, R.210 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.199, B:R.203 SO4.15: 3 residues within 4Å: Chain G: R.199, R.203, R.210 2 PLIP interactions: 2 interactions with chain G Salt bridges: G:R.199, G:R.203

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

CL.3: 3 residues within 4Å: Chain B: N.132, R.155, K.159 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain E: N.249, S.250, K.253 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain G: N.132, R.155, K.159 Ligand excluded by PLIP CL.23: 3 residues within 4Å: Chain J: N.249, S.250, K.253 Ligand excluded by PLIP

12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 6 residues within 4Å: Chain C: L.174, S.177, R.179, S.271 Chain E: N.7, M.9 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:S.177, C:R.179, C:R.179, C:S.271, E:N.7 EDO.6: 4 residues within 4Å: Chain C: E.204, N.211 Chain E: Y.35, R.37 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:E.204, C:N.211 Water bridges: E:E.36 EDO.7: 8 residues within 4Å: Chain B: P.17, Y.32, D.118, K.247, R.248 Chain C: L.232, A.233, E.238 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.118, B:K.247, B:R.248, B:R.248 Water bridges: B:Y.32, B:Y.32 EDO.9: 8 residues within 4Å: Chain C: F.18, E.19, R.51 Chain E: G.155, S.350, L.351, W.353 Chain G: K.223 5 PLIP interactions: 3 interactions with chain E, 1 interactions with chain C, 1 interactions with chain G Hydrogen bonds: E:S.350, E:L.351, E:W.353, C:E.19, G:K.223 EDO.11: 7 residues within 4Å: Chain E: I.68, V.69, T.70, G.71, T.110, V.111, R.112 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:R.112 Water bridges: E:V.69, E:V.69, E:R.112, E:R.112, E:R.112 EDO.12: 6 residues within 4Å: Chain E: T.232, K.233, K.240, K.295, Y.296, E.297 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:K.233, E:Y.296, E:E.297, E:E.297 EDO.18: 6 residues within 4Å: Chain H: L.174, S.177, R.179, S.271 Chain J: N.7, M.9 5 PLIP interactions: 4 interactions with chain H, 1 interactions with chain J Hydrogen bonds: H:S.177, H:R.179, H:R.179, H:S.271, J:N.7 EDO.19: 4 residues within 4Å: Chain H: E.204, N.211 Chain J: Y.35, R.37 3 PLIP interactions: 2 interactions with chain H, 1 interactions with chain J Hydrogen bonds: H:E.204, H:N.211 Water bridges: J:E.36 EDO.20: 8 residues within 4Å: Chain G: P.17, Y.32, D.118, K.247, R.248 Chain H: L.232, A.233, E.238 8 PLIP interactions: 2 interactions with chain H, 6 interactions with chain G Hydrogen bonds: H:E.238, G:Y.32, G:D.118, G:K.247, G:R.248, G:R.248 Water bridges: H:L.232, G:Y.32 EDO.22: 8 residues within 4Å: Chain B: K.223 Chain H: F.18, E.19, R.51 Chain J: G.155, S.350, L.351, W.353 4 PLIP interactions: 3 interactions with chain J, 1 interactions with chain B Hydrogen bonds: J:S.350, J:L.351, J:W.353, B:K.223 EDO.24: 7 residues within 4Å: Chain J: I.68, V.69, T.70, G.71, T.110, V.111, R.112 6 PLIP interactions: 6 interactions with chain J Hydrogen bonds: J:R.112 Water bridges: J:V.69, J:V.69, J:R.112, J:R.112, J:R.112 EDO.25: 6 residues within 4Å: Chain J: T.232, K.233, K.240, K.295, Y.296, E.297 3 PLIP interactions: 3 interactions with chain J Hydrogen bonds: J:K.233, J:Y.296, J:E.297

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.8: 20 residues within 4Å: Chain A: X.64, G.65, S.66 Chain D: R.117, P.121, S.122, G.123, A.125, M.209 Chain I: R.82, P.84, S.85, R.181, Y.218, R.233, V.234, W.235, A.236, G.237, I.258 22 PLIP interactions: 14 interactions with chain I, 5 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: I:V.234, I:V.234, I:A.236 Hydrogen bonds: I:S.85, I:S.85, I:S.85, I:S.85, I:R.181, I:R.181, I:R.233, I:R.233, I:A.236, I:G.237, D:S.122, D:A.125, A:S.66 Salt bridges: I:R.82, D:R.117 Water bridges: D:R.118, D:Y.127, A:G.65, A:S.66 FMN.21: 20 residues within 4Å: Chain D: R.82, P.84, S.85, R.181, Y.218, R.233, V.234, W.235, A.236, G.237, I.258 Chain F: X.64, G.65, S.66 Chain I: R.117, P.121, S.122, G.123, A.125, M.209 23 PLIP interactions: 15 interactions with chain D, 5 interactions with chain I, 3 interactions with chain F Hydrophobic interactions: D:V.234, D:V.234, D:A.236 Hydrogen bonds: D:S.85, D:S.85, D:S.85, D:S.85, D:R.181, D:R.181, D:R.233, D:R.233, D:A.236, D:G.237, I:S.122, I:A.125, F:S.66 Water bridges: D:D.178, I:Y.127, I:Y.127, F:G.65, F:S.66 Salt bridges: D:R.82, I:R.117

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 6 residues within 4Å: Chain E: G.53, G.56, E.57, E.60, S.152, F.153 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:G.53, E:F.153 Water bridges: E:E.60, E:S.152 GOL.26: 6 residues within 4Å: Chain J: G.53, G.56, E.57, E.60, S.152, F.153 5 PLIP interactions: 5 interactions with chain J Hydrogen bonds: J:G.53, J:E.60, J:F.153 Water bridges: J:E.60, J:S.152

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

Bacteriocin microcin B17: AF
Microcin B17-processing protein McbB: BCGH
Microcin B17-processing protein McbC: DI
Microcin B17-processing protein McbD: EJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

F
A

B
1

C
2

G
1

H
2

D
C

I
C

E
D

J
D

Bacteriocin microcin B17

Microcin B17-processing protein McbB

Microcin B17-processing protein McbC

Microcin B17-processing protein McbD

Related Entries With Identical Sequence